Notebook for the integration and pathway analysis of the VAE¶

In [1]:
import pandas as pd
import pandas as pd
from collections import defaultdict
import seaborn as sns
import numpy as np
from scivae import VAE
import warnings

warnings.filterwarnings("ignore")

base_dir = '../data/'
data_dir = f'{base_dir}sircle/F6_integrative_comparisons/'
output_dir = f'{base_dir}sircle/F6_integrative_comparisons/'
input_data_dir = f'{base_dir}sircle/F1_DE_input_TvN/'

fig_dir = '../figures/'
supp_dir = f'{base_dir}raw_downloads/supps/'
gene_name = 'hgnc_symbol'
save_fig = False
test_title = 'all_patients_ccRCC'

stats_base_dir = f'{output_dir}'
stats_stats_dir = f'{output_dir}'
stats_output_dir = f'{output_dir}'
stats_fig_dir = fig_dir
stats_vae_dir = f'{output_dir}VAE_configs/'

# Read in the data
stats_data_dir = data_dir

Load sample files and data, save input files¶

In [2]:
gene_id = 'ensembl_gene_id'
# Load in the files that we used for DE analysis and remove any redundent columns
# the VAE excpets just the ID as the index, and then the values
rna_sample_file = f'{input_data_dir}rna_sample_df_sircle_ccRCC.csv'
prot_sample_file = f'{input_data_dir}prot_sample_data_sircle_ccRCC.csv'
# Now we want to merge the clinical info with the cases from the sample df
meth_sample_file = f'{input_data_dir}cpg_sample_data_all_patients_ccRCC_sircle.csv'
tcga_cptac_clin = f'{input_data_dir}clinical_CPTAC_TCGA.csv'

rna_samples = list(pd.read_csv(rna_sample_file)['FullLabel'].values)
prot_samples = list(pd.read_csv(prot_sample_file)['FullLabel'].values)
meth_samples = list(pd.read_csv(meth_sample_file)['FullLabel'].values)
# Only use the filtered i.e. one CpG to one gene mapping for the cpg data
cpg_data_df = pd.read_csv(f'{base_dir}sircle/F2_DE_output_TvN/filtered_cpg_DE_all_patients_ccRCC_sircle.csv')
# Use this one as it has tmm normalised RNA 
rna_data_df = pd.read_csv(f'{base_dir}sircle/F2_DE_output_TvN/rna_DE_all_patients_ccRCC_sircle.csv')
prot_data_df = pd.read_csv(f'{base_dir}sircle/F2_DE_output_TvN/prot_DE_all_patients_ccRCC_sircle.csv')

cpg_data_df = cpg_data_df[[gene_id] + meth_samples]
rna_data_df = rna_data_df[[gene_id] + rna_samples]
protein_data_df = prot_data_df[[gene_id] + prot_samples]

rcm_df = pd.read_csv(f'{base_dir}sircle/F3_regulatory_clustering/RCM_all_patients_ccRCC_P0.5-R1.0-M0.1-GENES.csv')
# First filter out any NA values (we're not interested in non SiRCle genes)
rcm_df = rcm_df[rcm_df['Regulation_Grouping_2'] != 'None']

meta_cols = [gene_id, 'external_gene_name', 'entrezgene_id', 'hgnc_symbol', "logFC_rna", "padj_rna", 
             "CpG_Beta_diff", "padj_meth", "logFC_protein", "padj_protein", "Regulation_Grouping_2"]


# Save to input dir
save_input_data = False
meta_rcm_df = rcm_df[meta_cols].copy()
meta_rcm_df.set_index('ensembl_gene_id', inplace=True)
# Save to the input data dir folder.
if save_input_data:
    protein_data_df.to_csv(f'{stats_data_dir}CPTAC_protein.csv', index=False)
    rna_data_df.to_csv(f'{stats_data_dir}CPTAC_rna.csv', index=False)
    cpg_data_df.to_csv(f'{stats_data_dir}CPTAC_cpg.csv', index=False)
    meta_rcm_df.to_csv(f'{stats_data_dir}RCM.csv')

Run Integration¶

In [3]:
from scircm import RCMStats
missing_method='mean'
label = missing_method
sv = RCMStats(rcm_file=f'{stats_data_dir}RCM.csv', 
              patient_sample_file=tcga_cptac_clin,
              meth_file=f'{stats_data_dir}CPTAC_cpg.csv', 
              meth_sample_file=meth_sample_file, 
              rna_file=f'{stats_data_dir}CPTAC_rna.csv', 
              rna_sample_file=rna_sample_file,
              protein_file=f'{stats_data_dir}CPTAC_protein.csv', 
              protein_sample_file=prot_sample_file,
              output_folder=stats_vae_dir, 
              column_id='FullLabel',
              condition_column='CondId',
              patient_id_column='SafeCases',
              run_name=label,
              normalise='rows', 
              verbose=True,
             missing_method=missing_method)

--------------------------------------------------------------------------------
WARNING: you cannot have underscores in your case_id names. Please check this before usingthis tool.	
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Overlap between SiRCLe gene clusters and protein, RNA, and CpG: 	2788	
	If you used SiRCLe, this should be the total number of genes in your SiRCLe dataset. 6718	
 First 5 gene IDs in RCM: 	['ENSG00000188001', 'ENSG00000167656', 'ENSG00000182183', 'ENSG00000255071', 'ENSG00000180447']	
 First 5 gene IDs in Protein: 	[nan, 'ENSG00000167656', 'ENSG00000014138', 'ENSG00000255071', 'ENSG00000164885']	
 First 5 gene IDs in RNA: 	['ENSG00000258716', 'ENSG00000164885', 'ENSG00000235869', 'ENSG00000248506', 'ENSG00000227232']	
 First 5 gene IDs in Methylation: 	['ENSG00000167656', 'ENSG00000164885', 'ENSG00000186470', 'ENSG00000123560', 'ENSG00000180574']	
--------------------------------------------------------------------------------
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Had multiple samples for: 	C3L.00369	just took the first one.	['RNA_Tumor_C3L.00369_1' 'RNA_Tumor_C3L.00369_2' 'RNA_Tumor_C3L.00369_3']	
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Had multiple samples for: 	C3L.00418	just took the first one.	['RNA_Tumor_C3L.00418_1' 'RNA_Tumor_C3L.00418_2' 'RNA_Tumor_C3L.00418_3']	
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Had multiple samples for: 	C3L.00447	just took the first one.	['RNA_Tumor_C3L.00447_1' 'RNA_Tumor_C3L.00447_2' 'RNA_Tumor_C3L.00447_3']	
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Had multiple samples for: 	C3L.00581	just took the first one.	['RNA_Tumor_C3L.00581_1' 'RNA_Tumor_C3L.00581_2' 'RNA_Tumor_C3L.00581_3']	
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Had multiple samples for: 	C3L.00583	just took the first one.	['RNA_Tumor_C3L.00583_1' 'RNA_Tumor_C3L.00583_2' 'RNA_Tumor_C3L.00583_3']	
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Had multiple samples for: 	C3L.00606	just took the first one.	['RNA_Tumor_C3L.00606_1' 'RNA_Tumor_C3L.00606_2' 'RNA_Tumor_C3L.00606_3']	
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Had multiple samples for: 	C3L.00907	just took the first one.	['RNA_Tumor_C3L.00907_1' 'RNA_Tumor_C3L.00907_2' 'RNA_Tumor_C3L.00907_3']	
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Had multiple samples for: 	C3L.01286	just took the first one.	['RNA_Tumor_C3L.01286_1' 'RNA_Tumor_C3L.01286_2' 'RNA_Tumor_C3L.01286_3']	
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Had multiple samples for: 	C3L.01287	just took the first one.	['RNA_Tumor_C3L.01287_1' 'RNA_Tumor_C3L.01287_2']	
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Had multiple samples for: 	C3L.01603	just took the first one.	['RNA_Tumor_C3L.01603_1' 'RNA_Tumor_C3L.01603_2' 'RNA_Tumor_C3L.01603_3']	
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Had multiple samples for: 	C3L.01607	just took the first one.	['RNA_Tumor_C3L.01607_1' 'RNA_Tumor_C3L.01607_2' 'RNA_Tumor_C3L.01607_3']	
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Had multiple samples for: 	C3L.01836	just took the first one.	['RNA_Tumor_C3L.01836_1' 'RNA_Tumor_C3L.01836_2' 'RNA_Tumor_C3L.01836_3']	
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Had multiple samples for: 	C3N.00148	just took the first one.	['RNA_Tumor_C3N.00148_1' 'RNA_Tumor_C3N.00148_2' 'RNA_Tumor_C3N.00148_3'
 'RNA_Tumor_C3N.00148_4']	
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Had multiple samples for: 	C3N.00150	just took the first one.	['RNA_Tumor_C3N.00150_1' 'RNA_Tumor_C3N.00150_2' 'RNA_Tumor_C3N.00150_3'
 'RNA_Tumor_C3N.00150_4']	
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Had multiple samples for: 	C3N.00168	just took the first one.	['RNA_Tumor_C3N.00168_1' 'RNA_Tumor_C3N.00168_2' 'RNA_Tumor_C3N.00168_3'
 'RNA_Tumor_C3N.00168_4']	
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Had multiple samples for: 	C3N.00177	just took the first one.	['RNA_Tumor_C3N.00177_1' 'RNA_Tumor_C3N.00177_2' 'RNA_Tumor_C3N.00177_3']	
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Had multiple samples for: 	C3N.00194	just took the first one.	['RNA_Tumor_C3N.00194_1' 'RNA_Tumor_C3N.00194_2']	
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Had multiple samples for: 	C3N.00310	just took the first one.	['RNA_Tumor_C3N.00310_1' 'RNA_Tumor_C3N.00310_2' 'RNA_Tumor_C3N.00310_3']	
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Had multiple samples for: 	C3N.00312	just took the first one.	['RNA_Tumor_C3N.00312_1' 'RNA_Tumor_C3N.00312_2' 'RNA_Tumor_C3N.00312_3'
 'RNA_Tumor_C3N.00312_4']	
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Had multiple samples for: 	C3N.00314	just took the first one.	['RNA_Tumor_C3N.00314_1' 'RNA_Tumor_C3N.00314_2' 'RNA_Tumor_C3N.00314_3'
 'RNA_Tumor_C3N.00314_4']	
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Had multiple samples for: 	C3N.00317	just took the first one.	['RNA_Tumor_C3N.00317_1' 'RNA_Tumor_C3N.00317_2']	
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Had multiple samples for: 	C3N.00320	just took the first one.	['RNA_Tumor_C3N.00320_1' 'RNA_Tumor_C3N.00320_2' 'RNA_Tumor_C3N.00320_3']	
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Had multiple samples for: 	C3N.00390	just took the first one.	['RNA_Tumor_C3N.00390_1' 'RNA_Tumor_C3N.00390_2' 'RNA_Tumor_C3N.00390_3']	
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Had multiple samples for: 	C3N.00437	just took the first one.	['RNA_Tumor_C3N.00437_1' 'RNA_Tumor_C3N.00437_2' 'RNA_Tumor_C3N.00437_3']	
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Had multiple samples for: 	C3N.00494	just took the first one.	['RNA_Tumor_C3N.00494_1' 'RNA_Tumor_C3N.00494_2' 'RNA_Tumor_C3N.00494_3']	
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Had multiple samples for: 	C3N.00573	just took the first one.	['RNA_Tumor_C3N.00573_1' 'RNA_Tumor_C3N.00573_2' 'RNA_Tumor_C3N.00573_3'
 'RNA_Tumor_C3N.00573_4']	
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Had multiple samples for: 	C3N.00577	just took the first one.	['RNA_Tumor_C3N.00577_1' 'RNA_Tumor_C3N.00577_2' 'RNA_Tumor_C3N.00577_3']	
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Had multiple samples for: 	C3N.00646	just took the first one.	['RNA_Tumor_C3N.00646_1' 'RNA_Tumor_C3N.00646_2' 'RNA_Tumor_C3N.00646_3'
 'RNA_Tumor_C3N.00646_4']	
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Had multiple samples for: 	C3N.00733	just took the first one.	['RNA_Tumor_C3N.00733_1' 'RNA_Tumor_C3N.00733_2']	
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Had multiple samples for: 	C3N.00852	just took the first one.	['RNA_Tumor_C3N.00852_1' 'RNA_Tumor_C3N.00852_2']	
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Had multiple samples for: 	C3N.00953	just took the first one.	['RNA_Tumor_C3N.00953_1' 'RNA_Tumor_C3N.00953_2' 'RNA_Tumor_C3N.00953_3']	
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Had multiple samples for: 	C3N.01200	just took the first one.	['RNA_Tumor_C3N.01200_1' 'RNA_Tumor_C3N.01200_2' 'RNA_Tumor_C3N.01200_3'
 'RNA_Tumor_C3N.01200_4']	
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Had multiple samples for: 	C3N.01214	just took the first one.	['RNA_Tumor_C3N.01214_1' 'RNA_Tumor_C3N.01214_2' 'RNA_Tumor_C3N.01214_3']	
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Had multiple samples for: 	C3N.01220	just took the first one.	['RNA_Tumor_C3N.01220_1' 'RNA_Tumor_C3N.01220_2' 'RNA_Tumor_C3N.01220_3']	
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Had multiple samples for: 	C3N.01261	just took the first one.	['RNA_Tumor_C3N.01261_1' 'RNA_Tumor_C3N.01261_2']	
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Had multiple samples for: 	C3N.01522	just took the first one.	['RNA_Tumor_C3N.01522_1' 'RNA_Tumor_C3N.01522_2' 'RNA_Tumor_C3N.01522_3']	
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Had multiple samples for: 	C3N.01524	just took the first one.	['RNA_Tumor_C3N.01524_1' 'RNA_Tumor_C3N.01524_2' 'RNA_Tumor_C3N.01524_3']	
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Look at the missing vs matched data¶

In [4]:
# Get the patient info that has been compiled from the provided sample files
patient_info = sv.patient_clinical_df
# Select the cases with 5 samples 
matching_patient_info = patient_info[patient_info['Sample counts'] == 5]
matching_cases = matching_patient_info['SafeCases'].values
print("total number of patients: ", len(patient_info), " vs number with matching data: ", len(matching_patient_info))
matching_cases

total number of patients:  261  vs number with matching data:  59
Out[4]:
array(['C3L.00004', 'C3L.00010', 'C3L.00011', 'C3L.00026', 'C3L.00079',
       'C3L.00088', 'C3L.00096', 'C3L.00097', 'C3L.00103', 'C3L.00360',
       'C3L.00369', 'C3L.00416', 'C3L.00418', 'C3L.00447', 'C3L.00581',
       'C3L.00606', 'C3L.00814', 'C3L.00902', 'C3L.00907', 'C3L.00908',
       'C3L.00910', 'C3L.00917', 'C3L.01286', 'C3L.01287', 'C3L.01313',
       'C3L.01603', 'C3L.01607', 'C3L.01836', 'C3N.00148', 'C3N.00149',
       'C3N.00150', 'C3N.00177', 'C3N.00194', 'C3N.00244', 'C3N.00310',
       'C3N.00314', 'C3N.00390', 'C3N.00494', 'C3N.00495', 'C3N.00573',
       'C3N.00577', 'C3N.00646', 'C3N.00733', 'C3N.00831', 'C3N.00834',
       'C3N.00852', 'C3N.01176', 'C3N.01178', 'C3N.01179', 'C3N.01200',
       'C3N.01214', 'C3N.01220', 'C3N.01261', 'C3N.01361', 'C3N.01522',
       'C3N.01646', 'C3N.01649', 'C3N.01651', 'C3N.01808'], dtype=object)

Ensure that the old people aren't all stage 4¶

Plot demographics for the input data

In [5]:
cptac = patient_info[~patient_info['case_id'].isnull()]
old = cptac[cptac['AgeGrouped'] == 'old']
young = cptac[cptac['AgeGrouped'] == 'young']
# Now do the number / percent stage 1 and stage 4
s4 = old[old['TumorStage'] == 'Stage IV']
s2 = old[old['TumorStage'] == 'Stage II']
s3 = old[old['TumorStage'] == 'Stage III']
s1 = old[old['TumorStage'] == 'Stage I']
print(len(s1), len(s2), len(s3), len(s4))
print(len(s1)/len(old), len(s2)/len(old), len(s3)/len(old), len(s4)/len(old))

# Now do the number / percent stage 1 and stage 4
s4 = young[young['TumorStage'] == 'Stage IV']
s2 = young[young['TumorStage'] == 'Stage II']
s3 = young[young['TumorStage'] == 'Stage III']
s1 = young[young['TumorStage'] == 'Stage I']
print(len(s1), len(s2), len(s3), len(s4))
print(len(s1)/len(young), len(s2)/len(young), len(s3)/len(young), len(s4)/len(young))

27 9 24 6
0.4090909090909091 0.13636363636363635 0.36363636363636365 0.09090909090909091
7 1 1 0
0.7777777777777778 0.1111111111111111 0.1111111111111111 0.0
In [6]:
import matplotlib.pyplot as plt

palette = ['#483873', '#1BD8A6', '#B117B7', '#AAC7E2', '#FFC107', '#016957', '#9785C0',
     '#D09139', '#338A03', '#FF69A1', '#5930B1', '#FFE884', '#35B567', '#1E88E5',
     '#ACAD60', '#A2FFB4', '#B618F5', '#854A9C']
plt.rcParams['svg.fonttype'] = 'none'  # Ensure text is saved as text
plt.rcParams['figure.figsize'] = (3, 2)
sns.set(rc={'figure.figsize': (3, 2), 'font.family': 'sans-serif',
            'font.sans-serif': 'Arial', 'font.size': 9}, style='ticks')

g = sns.catplot(x="Stage", hue="AgeGrouped", col="gender",
                order=['Early', 'Late'],
                data=patient_info, kind="count", palette='Greys', hue_order=['young', 'middle', 'old'],
                height=4, aspect=.7)
plt.xticks(rotation=45, ha='right')
plt.savefig(f'{stats_fig_dir}patient_demographics_all.svg')
plt.show()

g = sns.catplot(x="Stage", hue="AgeGrouped", col="gender",
                order=['Early', 'Late'],
                data=matching_patient_info, kind="count", palette='Greys', hue_order=['young', 'middle', 'old'],
                height=4, aspect=.7)
plt.xticks(rotation=45, ha='right')
plt.savefig(f'{stats_fig_dir}patient_demographics_matched.svg')
plt.show()

g = sns.catplot(x="Stage", hue="AgeGrouped", col="BAP1&PBRM1",
                order=['Early', 'Late'],
                data=patient_info, kind="count", palette='Greys', hue_order=['young', 'middle', 'old'],
                height=4, aspect=.7)
plt.xticks(rotation=45, ha='right')
plt.savefig(f'{stats_fig_dir}patient_demographics_BAP1&PBRM1_all.svg')
plt.show()

g = sns.countplot(x="Stage", hue="AgeGrouped",
                order=['Early', 'Late'],
                data=matching_patient_info)
plt.xticks(rotation=45, ha='right')


g = sns.catplot(x="TumorStage", hue="AgeGrouped", col="BAP1&PBRM1", hue_order=['young', 'middle', 'old'],
                data=patient_info, kind="count", palette='Greys', order=['Stage I', 'Stage II', 'Stage III', 'Stage IV'],
                height=4, aspect=.7)
plt.xticks(rotation=45, ha='right')
plt.savefig(f'{stats_fig_dir}patient_demographics_BAP1&PBRM1.svg')
plt.show()

Train integration model (VAE)¶

In [7]:
train = False
if train:
    epochs = 100 
    batch_size = 16
    num_nodes = 5
    mmd_weight = 0.25
    loss = {'loss_type': 'mse', 'distance_metric': 'mmd', 'mmd_weight': mmd_weight}
    config = {"loss": loss,
              "encoding": {"layers": [{"num_nodes": num_nodes, "activation_fn": "relu"}]},
              "decoding": {"layers": [{"num_nodes": num_nodes, "activation_fn": "relu"}]},
              "latent": {"num_nodes": 1},
              "optimiser": {"params": {'learning_rate': 0.01}, "name": "adam"},
              "epochs": epochs,
              "batch_size": batch_size,
              "scale_data": False
              }
    training_cases = matching_cases # Use matching cases for training
    sv.train_vae(cases=matching_cases, config=config)
    sv.save()  # Save the information we have generated.
else:
    sv.load_saved_vaes()
    sv.load_saved_encodings(f'{sv.output_folder}encoded_df_{label}.csv')
    sv.load_saved_inputs(f'{sv.output_folder}vae_input_df_{label}.csv')
    sv.load_saved_raws(f'{sv.output_folder}raw_input_df_{label}.csv')

7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense (Dense)                  (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense[0][0]']                  
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense[0][0]']                  
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_1 (Dense)             (None, 5)                 10        
                                                                 
 dense_2 (Dense)             (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None

2022-06-07 11:05:11.817181: I tensorflow/core/platform/cpu_feature_guard.cc:193] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations:  AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.

7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_3 (Dense)                (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_3[0][0]']                
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_3[0][0]']                
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_4 (Dense)             (None, 5)                 10        
                                                                 
 dense_5 (Dense)             (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None
7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_6 (Dense)                (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_6[0][0]']                
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_6[0][0]']                
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_7 (Dense)             (None, 5)                 10        
                                                                 
 dense_8 (Dense)             (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None
7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_9 (Dense)                (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_9[0][0]']                
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_9[0][0]']                
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_10 (Dense)            (None, 5)                 10        
                                                                 
 dense_11 (Dense)            (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None
7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_12 (Dense)               (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_12[0][0]']               
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_12[0][0]']               
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_13 (Dense)            (None, 5)                 10        
                                                                 
 dense_14 (Dense)            (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None
7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_15 (Dense)               (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_15[0][0]']               
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_15[0][0]']               
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_16 (Dense)            (None, 5)                 10        
                                                                 
 dense_17 (Dense)            (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None
7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_18 (Dense)               (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_18[0][0]']               
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_18[0][0]']               
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_19 (Dense)            (None, 5)                 10        
                                                                 
 dense_20 (Dense)            (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None
7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_21 (Dense)               (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_21[0][0]']               
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_21[0][0]']               
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_22 (Dense)            (None, 5)                 10        
                                                                 
 dense_23 (Dense)            (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None
7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_24 (Dense)               (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_24[0][0]']               
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_24[0][0]']               
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_25 (Dense)            (None, 5)                 10        
                                                                 
 dense_26 (Dense)            (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None
7
--------------------------------------------------------------------------------
                               Encoder summary:	                                
--------------------------------------------------------------------------------
Model: "encoder"
__________________________________________________________________________________________________
 Layer (type)                   Output Shape         Param #     Connected to                     
==================================================================================================
 default_input (InputLayer)     [(None, 7)]          0           []                               
                                                                                                  
 dense_27 (Dense)               (None, 5)            40          ['default_input[0][0]']          
                                                                                                  
 z_mean (Dense)                 (None, 1)            6           ['dense_27[0][0]']               
                                                                                                  
 z_log_sigma (Dense)            (None, 1)            6           ['dense_27[0][0]']               
                                                                                                  
 z (Lambda)                     (None, 1)            0           ['z_mean[0][0]',                 
                                                                  'z_log_sigma[0][0]']            
                                                                                                  
==================================================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
__________________________________________________________________________________________________
None
--------------------------------------------------------------------------------
                               Decoder summary:	                                
--------------------------------------------------------------------------------
Model: "decoder"
_________________________________________________________________
 Layer (type)                Output Shape              Param #   
=================================================================
 z_sampling (InputLayer)     [(None, 1)]               0         
                                                                 
 dense_28 (Dense)            (None, 5)                 10        
                                                                 
 dense_29 (Dense)            (None, 7)                 42        
                                                                 
=================================================================
Total params: 52
Trainable params: 52
Non-trainable params: 0
_________________________________________________________________
None

Run stats on different comparisons!¶

In [8]:
from sciutil import SciUtil
u = SciUtil()
u.warn_p(['AgeGrouped'])
sv.run_vae_stats(cond_label='AgeGrouped', cond0='young', cond1='old')

u.warn_p(['Mutation'])
sv.run_vae_stats(cond_label='BAP1&PBRM1', cond0='BAP1', cond1='PBRM1')

u.warn_p(['S4 vs S1'])
sv.run_vae_stats(cond_label='TumorStage', cond0='Stage I', cond1='Stage IV')

--------------------------------------------------------------------------------
                                  AgeGrouped	                                   
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                    1420.000000                  1420.000000   
mean                      222.261972                     0.933186   
std                        51.317501                     0.068463   
min                        79.000000                     0.639473   
25%                       188.000000                     0.893602   
50%                       223.000000                     0.954762   
75%                       258.250000                     0.986121   
max                       372.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                  1420.000000                  1420.000000   
mean                      0.490597                    -0.003830   
std                       0.294965                     0.189493   
min                       0.001672                    -0.747490   
25%                       0.231924                    -0.110745   
50%                       0.490876                    -0.011870   
75%                       0.742369                     0.099190   
max                       1.000000                     0.785683   

       Integrated mean (young)  Integrated mean (old)  
count              1420.000000            1420.000000  
mean                  0.048690               0.044860  
std                   0.770364               0.726576  
min                  -1.941687              -1.839760  
25%                  -0.406316              -0.361654  
50%                  -0.037527              -0.078767  
75%                   0.316689               0.187991  
max                   2.048632               1.980273  	
--------------------------------------------------------------------------------
TPDS_TMDE Integrated mean (young): NOT normally distributed
TPDS_TMDE Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                    1069.000000                  1069.000000   
mean                      209.865295                     0.770432   
std                        56.929622                     0.197536   
min                        55.000000                     0.231230   
25%                       171.000000                     0.677043   
50%                       210.000000                     0.829290   
75%                       249.000000                     0.934431   
max                       369.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                  1069.000000                  1069.000000   
mean                      0.443276                    -0.041484   
std                       0.302310                     0.154796   
min                       0.000216                    -0.674443   
25%                       0.173881                    -0.128795   
50%                       0.418136                    -0.026541   
75%                       0.712405                     0.058096   
max                       1.000000                     0.508046   

       Integrated mean (young)  Integrated mean (old)  
count              1069.000000            1069.000000  
mean                 -0.126007              -0.167492  
std                   0.830104               0.831869  
min                  -1.353714              -1.286995  
25%                  -0.783881              -0.816976  
50%                  -0.359374              -0.461596  
75%                   0.805239               0.815412  
max                   1.715993               1.701468  	
--------------------------------------------------------------------------------
TPDE_TMDS Integrated mean (young): NOT normally distributed
TPDE_TMDS Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                     313.000000                   313.000000   
mean                      203.492013                     0.668432   
std                        58.979685                     0.199788   
min                        69.000000                     0.123924   
25%                       161.000000                     0.513374   
50%                       200.000000                     0.652299   
75%                       252.000000                     0.830456   
max                       356.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                   313.000000                   313.000000   
mean                      0.395285                    -0.091849   
std                       0.291038                     0.292004   
min                       0.000896                    -1.078334   
25%                       0.132341                    -0.284512   
50%                       0.331360                    -0.095850   
75%                       0.625197                     0.131234   
max                       1.000000                     0.772396   

       Integrated mean (young)  Integrated mean (old)  
count               313.000000             313.000000  
mean                  0.105253               0.013403  
std                   0.584182               0.541674  
min                  -2.001875              -1.914269  
25%                  -0.259332              -0.368499  
50%                   0.149075               0.106208  
75%                   0.489664               0.424285  
max                   1.515369               1.167666  	
--------------------------------------------------------------------------------
TMDE Integrated mean (young): NOT normally distributed
TMDE Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                     803.000000                   803.000000   
mean                      276.201743                     0.385017   
std                        62.578164                     0.259215   
min                        63.000000                     0.014704   
25%                       243.000000                     0.173410   
50%                       286.000000                     0.321127   
75%                       320.000000                     0.532627   
max                       412.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                   803.000000                   803.000000   
mean                      0.266404                     0.245015   
std                       0.274010                     0.324696   
min                       0.000018                    -1.074049   
25%                       0.044054                     0.072088   
50%                       0.161163                     0.274438   
75%                       0.400980                     0.455982   
max                       1.000000                     1.375791   

       Integrated mean (young)  Integrated mean (old)  
count               803.000000             803.000000  
mean                 -0.220406               0.024609  
std                   0.735315               0.619668  
min                  -2.116405              -1.357285  
25%                  -0.717126              -0.432557  
50%                  -0.280204              -0.057173  
75%                   0.219129               0.394617  
max                   2.398970               2.153304  	
--------------------------------------------------------------------------------
TMDS Integrated mean (young): NOT normally distributed
TMDS Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                     539.000000                   539.000000   
mean                      250.530612                     0.683886   
std                        54.735597                     0.172350   
min                        81.000000                     0.396896   
25%                       208.000000                     0.551028   
50%                       257.000000                     0.681829   
75%                       291.500000                     0.817606   
max                       368.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                   539.000000                   539.000000   
mean                      0.395653                     0.173275   
std                       0.289174                     0.392225   
min                       0.002336                    -1.099820   
25%                       0.140573                    -0.105316   
50%                       0.341547                     0.221693   
75%                       0.618149                     0.452459   
max                       1.000000                     1.398373   

       Integrated mean (young)  Integrated mean (old)  
count               539.000000             539.000000  
mean                 -0.075385               0.097890  
std                   0.760496               0.688098  
min                  -2.970549              -2.740273  
25%                  -0.535802              -0.249099  
50%                  -0.068381               0.172698  
75%                   0.457778               0.568858  
max                   1.915523               1.718554  	
--------------------------------------------------------------------------------
TPDS Integrated mean (young): NOT normally distributed
TPDS Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                     415.000000                   415.000000   
mean                      271.493976                     0.421486   
std                        65.746434                     0.308457   
min                        82.000000                     0.068662   
25%                       221.000000                     0.132398   
50%                       281.000000                     0.346926   
75%                       327.000000                     0.687005   
max                       383.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                   415.000000                   415.000000   
mean                      0.299522                    -0.218020   
std                       0.310466                     0.315853   
min                       0.000613                    -0.983795   
25%                       0.033817                    -0.446834   
50%                       0.173881                    -0.240644   
75%                       0.516495                     0.017580   
max                       1.000000                     0.610423   

       Integrated mean (young)  Integrated mean (old)  
count               415.000000             415.000000  
mean                  0.077109              -0.140911  
std                   0.451722               0.361264  
min                  -1.584353              -1.327478  
25%                  -0.200777              -0.345453  
50%                   0.110712              -0.105236  
75%                   0.393318               0.088686  
max                   1.074873               1.113607  	
--------------------------------------------------------------------------------
MDE Integrated mean (young): NOT normally distributed
MDE Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                     257.000000                   257.000000   
mean                      179.284047                     0.485419   
std                        62.337547                     0.311047   
min                        30.000000                     0.001768   
25%                       131.000000                     0.193922   
50%                       171.000000                     0.454997   
75%                       224.000000                     0.776763   
max                       344.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                   257.000000                   257.000000   
mean                      0.333660                    -0.243507   
std                       0.320233                     0.346243   
min                       0.000007                    -1.229605   
25%                       0.051310                    -0.492188   
50%                       0.231924                    -0.225928   
75%                       0.583328                    -0.008641   
max                       1.000000                     0.682164   

       Integrated mean (young)  Integrated mean (old)  
count               257.000000             257.000000  
mean                  0.134285              -0.109223  
std                   0.542793               0.462282  
min                  -1.520224              -1.527887  
25%                  -0.200261              -0.378527  
50%                   0.153863              -0.072534  
75%                   0.508885               0.194505  
max                   1.495358               1.280142  	
--------------------------------------------------------------------------------
TPDE Integrated mean (young): NOT normally distributed
TPDE Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                    1308.000000                  1308.000000   
mean                      247.435015                     0.686435   
std                        57.998466                     0.223175   
min                        52.000000                     0.049690   
25%                       205.000000                     0.483380   
50%                       248.000000                     0.740832   
75%                       293.250000                     0.888300   
max                       407.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                  1308.000000                  1308.000000   
mean                      0.410341                     0.066971   
std                       0.306114                     0.184857   
min                       0.000038                    -0.537729   
25%                       0.121954                    -0.067711   
50%                       0.373248                     0.059475   
75%                       0.668263                     0.191736   
max                       1.000000                     0.611403   

       Integrated mean (young)  Integrated mean (old)  
count              1308.000000            1308.000000  
mean                  0.513067               0.580039  
std                   1.044463               0.983080  
min                  -0.969205              -0.932439  
25%                  -0.263937              -0.118848  
50%                   0.178823               0.240338  
75%                   1.441019               1.463751  
max                   3.622106               3.498537  	
--------------------------------------------------------------------------------
MDE_TMDS Integrated mean (young): NOT normally distributed
MDE_TMDS Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                     131.000000                   131.000000   
mean                      212.656489                     0.712683   
std                        59.155047                     0.209073   
min                        91.000000                     0.097282   
25%                       167.000000                     0.507832   
50%                       214.000000                     0.750274   
75%                       253.500000                     0.933251   
max                       381.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                   131.000000                   131.000000   
mean                      0.423512                    -0.076454   
std                       0.309973                     0.312944   
min                       0.000743                    -1.004244   
25%                       0.143371                    -0.280692   
50%                       0.395322                    -0.049140   
75%                       0.712405                     0.141001   
max                       1.000000                     0.838019   

       Integrated mean (young)  Integrated mean (old)  
count               131.000000             131.000000  
mean                  0.127795               0.051341  
std                   0.657638               0.609409  
min                  -1.701344              -1.761892  
25%                  -0.360623              -0.284686  
50%                   0.139985               0.056952  
75%                   0.647476               0.479532  
max                   1.457658               1.212816  	
--------------------------------------------------------------------------------
MDS Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 56 vs Cond0: 8
	       mannwhitneyu stat (old-young)  Integrated padj (old-young)  \
count                     463.000000                   463.000000   
mean                      201.786177                     0.732877   
std                        57.136122                     0.231689   
min                        57.000000                     0.099678   
25%                       163.000000                     0.630263   
50%                       201.000000                     0.804586   
75%                       242.000000                     0.919029   
max                       359.000000                     1.000000   

       Integrated pval (old-young)  Integrated diff (old-young)  \
count                   463.000000                   463.000000   
mean                      0.433959                    -0.119217   
std                       0.305587                     0.233224   
min                       0.000269                    -0.821770   
25%                       0.161163                    -0.263856   
50%                       0.406637                    -0.088908   
75%                       0.697579                     0.020180   
max                       1.000000                     0.539676   

       Integrated mean (young)  Integrated mean (old)  
count               463.000000             463.000000  
mean                  0.119429               0.000212  
std                   0.760733               0.795969  
min                  -1.580338              -1.734891  
25%                  -0.383509              -0.526085  
50%                  -0.027600              -0.209923  
75%                   0.332835               0.139012  
max                   2.064413               2.022199  	
--------------------------------------------------------------------------------
MDS_TMDE Integrated mean (young): NOT normally distributed
MDS_TMDE Integrated mean (old): NOT normally distributed
--------------------------------------------------------------------------------
                                   Mutation	                                    
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                     1420.000000                   1420.000000   
mean                       211.435915                      0.647174   
std                         57.003895                      0.276343   
min                          6.000000                      0.000552   
25%                        174.000000                      0.472458   
50%                        212.000000                      0.724253   
75%                        251.000000                      0.879938   
max                        398.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                  1.420000e+03                   1420.000000   
mean                   4.051770e-01                     -0.016508   
std                    3.107984e-01                      0.240597   
min                    3.889192e-07                     -1.307524   
25%                    1.184473e-01                     -0.136284   
50%                    3.667168e-01                     -0.009702   
75%                    6.605729e-01                      0.098948   
max                    1.000000e+00                      1.358737   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count             1420.000000              1420.000000  
mean                 0.060012                 0.043504  
std                  0.731631                 0.736650  
min                 -1.823087                -1.803238  
25%                 -0.385498                -0.390405  
50%                 -0.044593                -0.085374  
75%                  0.291939                 0.201935  
max                  1.992189                 2.030184  	
--------------------------------------------------------------------------------
TPDS_TMDE Integrated mean (BAP1): NOT normally distributed
TPDS_TMDE Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                     1069.000000                   1069.000000   
mean                       213.859682                      0.470629   
std                         67.706163                      0.295635   
min                          7.000000                      0.000473   
25%                        165.000000                      0.202590   
50%                        218.000000                      0.456609   
75%                        264.000000                      0.720556   
max                        386.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                  1.069000e+03                   1069.000000   
mean                   3.228968e-01                      0.000132   
std                    3.005303e-01                      0.202758   
min                    4.420249e-07                     -1.095145   
25%                    5.097919e-02                     -0.120929   
50%                    2.319352e-01                      0.009034   
75%                    5.419332e-01                      0.121346   
max                    1.000000e+00                      0.679941   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count             1069.000000              1069.000000  
mean                -0.156558                -0.156426  
std                  0.826344                 0.830394  
min                 -1.315168                -1.304375  
25%                 -0.813609                -0.825298  
50%                 -0.424591                -0.442317  
75%                  0.784987                 0.826570  
max                  1.750236                 1.710146  	
--------------------------------------------------------------------------------
TPDE_TMDS Integrated mean (BAP1): NOT normally distributed
TPDE_TMDS Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                      313.000000                    313.000000   
mean                       206.805112                      0.458439   
std                         68.831341                      0.300420   
min                         20.000000                      0.000391   
25%                        155.000000                      0.173494   
50%                        203.000000                      0.459467   
75%                        258.000000                      0.721809   
max                        396.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                    313.000000                    313.000000   
mean                       0.318337                     -0.043556   
std                        0.302209                      0.397334   
min                        0.000002                     -1.475379   
25%                        0.045452                     -0.274214   
50%                        0.231935                     -0.040217   
75%                        0.541933                      0.229530   
max                        1.000000                      1.137583   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count              313.000000               313.000000  
mean                 0.053641                 0.010085  
std                  0.610276                 0.561982  
min                 -1.772228                -2.085427  
25%                 -0.350247                -0.343706  
50%                  0.047926                 0.088486  
75%                  0.499532                 0.427474  
max                  1.534708                 1.187935  	
--------------------------------------------------------------------------------
TMDE Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                      803.000000                    803.000000   
mean                       201.438356                      0.508041   
std                         64.853256                      0.310917   
min                         12.000000                      0.000667   
25%                        155.000000                      0.237425   
50%                        200.000000                      0.497520   
75%                        246.000000                      0.807558   
max                        377.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                  8.030000e+02                    803.000000   
mean                   3.463774e-01                     -0.035353   
std                    3.134513e-01                      0.348489   
min                    8.310592e-07                     -1.090203   
25%                    6.031719e-02                     -0.261538   
50%                    2.515481e-01                     -0.044348   
75%                    6.084345e-01                      0.170750   
max                    1.000000e+00                      1.250648   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count              803.000000               803.000000  
mean                 0.008592                -0.026761  
std                  0.668805                 0.643233  
min                 -1.793969                -1.651575  
25%                 -0.471813                -0.508675  
50%                 -0.054870                -0.074752  
75%                  0.422243                 0.356186  
max                  2.095483                 2.265657  	
--------------------------------------------------------------------------------
TMDS Integrated mean (BAP1): NOT normally distributed
TMDS Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                      539.000000                    539.000000   
mean                       203.712430                      0.559955   
std                         66.264094                      0.352065   
min                         32.000000                      0.001353   
25%                        158.000000                      0.210707   
50%                        206.000000                      0.621717   
75%                        242.500000                      0.926670   
max                        399.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                    539.000000                    539.000000   
mean                       0.383281                     -0.090012   
std                        0.332185                      0.573232   
min                        0.000007                     -2.144847   
25%                        0.053947                     -0.392351   
50%                        0.317203                     -0.019088   
75%                        0.696292                      0.232629   
max                        1.000000                      2.034626   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count              539.000000               539.000000  
mean                 0.101081                 0.011070  
std                  0.759355                 0.722810  
min                 -2.838331                -2.730878  
25%                 -0.377916                -0.419551  
50%                  0.132324                 0.038795  
75%                  0.620049                 0.488640  
max                  2.797310                 1.928402  	
--------------------------------------------------------------------------------
TPDS Integrated mean (BAP1): NOT normally distributed
TPDS Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                      415.000000                    415.000000   
mean                       233.946988                      0.414879   
std                         67.408461                      0.296828   
min                         41.000000                      0.005059   
25%                        186.500000                      0.149217   
50%                        244.000000                      0.355068   
75%                        285.000000                      0.637492   
max                        394.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                    415.000000                    415.000000   
mean                       0.293611                     -0.089818   
std                        0.299616                      0.340600   
min                        0.000013                     -1.489131   
25%                        0.038113                     -0.307648   
50%                        0.179673                     -0.137078   
75%                        0.479271                      0.132980   
max                        1.000000                      1.043621   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count              415.000000               415.000000  
mean                -0.053647                -0.143465  
std                  0.391555                 0.395650  
min                 -1.625804                -1.528071  
25%                 -0.267128                -0.376488  
50%                 -0.018497                -0.100035  
75%                  0.209086                 0.106013  
max                  1.055517                 0.972513  	
--------------------------------------------------------------------------------
MDE Integrated mean (BAP1): NOT normally distributed
MDE Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                      257.000000                    257.000000   
mean                       208.937743                      0.383163   
std                         73.310955                      0.306613   
min                         49.000000                      0.001462   
25%                        152.000000                      0.098081   
50%                        203.000000                      0.285419   
75%                        264.000000                      0.651800   
max                        401.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                    257.000000                    257.000000   
mean                       0.279811                     -0.026099   
std                        0.299453                      0.450607   
min                        0.000006                     -1.277391   
25%                        0.024806                     -0.361047   
50%                        0.143265                     -0.066706   
75%                        0.494557                      0.272922   
max                        1.000000                      1.505993   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count              257.000000               257.000000  
mean                -0.066877                -0.092976  
std                  0.551952                 0.495781  
min                 -1.748636                -1.732282  
25%                 -0.446891                -0.369507  
50%                  0.012463                -0.061378  
75%                  0.332758                 0.199427  
max                  0.983238                 1.356011  	
--------------------------------------------------------------------------------
TPDE Integrated mean (BAP1): NOT normally distributed
TPDE Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                     1308.000000                   1308.000000   
mean                       224.196483                      0.467611   
std                         67.826585                      0.306078   
min                         36.000000                      0.000616   
25%                        176.000000                      0.198455   
50%                        228.000000                      0.421708   
75%                        275.000000                      0.743527   
max                        417.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                  1.308000e+03                   1308.000000   
mean                   3.240647e-01                      0.029891   
std                    3.087643e-01                      0.228001   
min                    8.310592e-07                     -0.847713   
25%                    5.097919e-02                     -0.119488   
50%                    2.134333e-01                      0.038980   
75%                    5.582139e-01                      0.183209   
max                    1.000000e+00                      1.028562   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count             1308.000000              1308.000000  
mean                 0.549556                 0.579446  
std                  0.995770                 0.990930  
min                 -0.892479                -0.917921  
25%                 -0.173007                -0.130976  
50%                  0.227393                 0.234948  
75%                  1.427497                 1.461438  
max                  3.622638                 3.594970  	
--------------------------------------------------------------------------------
MDE_TMDS Integrated mean (BAP1): NOT normally distributed
MDE_TMDS Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                      131.000000                    131.000000   
mean                       214.641221                      0.481823   
std                         70.271350                      0.338775   
min                         48.000000                      0.005470   
25%                        169.500000                      0.153554   
50%                        215.000000                      0.460356   
75%                        267.500000                      0.764419   
max                        368.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                    131.000000                    131.000000   
mean                       0.342531                     -0.026057   
std                        0.329060                      0.449144   
min                        0.000051                     -2.036792   
25%                        0.039276                     -0.222388   
50%                        0.231935                      0.016151   
75%                        0.574843                      0.258593   
max                        1.000000                      1.023557   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count              131.000000               131.000000  
mean                 0.038725                 0.012669  
std                  0.639144                 0.613803  
min                 -1.835036                -1.738074  
25%                 -0.281083                -0.365748  
50%                  0.081625                 0.066338  
75%                  0.486612                 0.383143  
max                  1.636786                 1.238371  	
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Summary
	Cond1: 33 vs Cond0: 13
	       mannwhitneyu stat (PBRM1-BAP1)  Integrated padj (PBRM1-BAP1)  \
count                      463.000000                    463.000000   
mean                       222.177106                      0.649914   
std                         57.680818                      0.312156   
min                         58.000000                      0.029255   
25%                        187.500000                      0.384387   
50%                        221.000000                      0.728712   
75%                        258.500000                      0.960587   
max                        377.000000                      1.000000   

       Integrated pval (PBRM1-BAP1)  Integrated diff (PBRM1-BAP1)  \
count                    463.000000                    463.000000   
mean                       0.417797                      0.021734   
std                        0.328866                      0.250007   
min                        0.000077                     -0.721660   
25%                        0.097135                     -0.122931   
50%                        0.366717                      0.018379   
75%                        0.732697                      0.136030   
max                        1.000000                      0.899689   

       Integrated mean (BAP1)  Integrated mean (PBRM1)  
count              463.000000               463.000000  
mean                -0.014635                 0.007099  
std                  0.796475                 0.807312  
min                 -1.865031                -1.713511  
25%                 -0.566146                -0.540847  
50%                 -0.219106                -0.191867  
75%                  0.216450                 0.193497  
max                  2.058091                 2.046231  	
--------------------------------------------------------------------------------
MDS_TMDE Integrated mean (BAP1): NOT normally distributed
MDS_TMDE Integrated mean (PBRM1): NOT normally distributed
--------------------------------------------------------------------------------
                                   S4 vs S1	                                    
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                           1420.000000   
mean                             226.879577   
std                               71.709177   
min                               48.000000   
25%                              176.750000   
50%                              228.500000   
75%                              279.000000   
max                              415.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                         1420.000000                         1420.000000   
mean                             0.517078                            0.346292   
std                              0.295839                            0.303793   
min                              0.028431                            0.000035   
25%                              0.266248                            0.068437   
50%                              0.536390                            0.270462   
75%                              0.780280                            0.592903   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                         1420.000000                1420.000000   
mean                             0.002717                   0.052995   
std                              0.277265                   0.746992   
min                             -1.028620                  -1.813484   
25%                             -0.161417                  -0.374718   
50%                              0.004754                  -0.066306   
75%                              0.170749                   0.230399   
max                              0.793423                   2.007147   

       Integrated mean (Stage IV)  
count                 1420.000000  
mean                     0.055712  
std                      0.702168  
min                     -1.797110  
25%                     -0.381629  
50%                     -0.077396  
75%                      0.198627  
max                      2.030891  	
--------------------------------------------------------------------------------
TPDS_TMDE Integrated mean (Stage I): NOT normally distributed
TPDS_TMDE Integrated mean (Stage IV): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                           1069.000000   
mean                             233.931712   
std                               76.340149   
min                               48.000000   
25%                              175.000000   
50%                              235.000000   
75%                              290.000000   
max                              434.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                         1069.000000                         1069.000000   
mean                             0.456846                            0.319378   
std                              0.309729                            0.307709   
min                              0.005739                            0.000005   
25%                              0.164804                            0.041317   
50%                              0.418745                            0.209568   
75%                              0.748668                            0.563077   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                         1069.000000                1069.000000   
mean                             0.018361                  -0.163351   
std                              0.231087                   0.836972   
min                             -0.766239                  -1.344041   
25%                             -0.105226                  -0.818052   
50%                              0.027279                  -0.436337   
75%                              0.153386                   0.823151   
max                              0.747891                   1.684624   

       Integrated mean (Stage IV)  
count                 1069.000000  
mean                    -0.144990  
std                      0.838504  
min                     -1.322394  
25%                     -0.802781  
50%                     -0.453402  
75%                      0.815986  
max                      1.757009  	
--------------------------------------------------------------------------------
TPDE_TMDS Integrated mean (Stage I): NOT normally distributed
TPDE_TMDS Integrated mean (Stage IV): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                            313.000000   
mean                             224.939297   
std                               74.703170   
min                               52.000000   
25%                              168.000000   
50%                              224.000000   
75%                              277.000000   
max                              390.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                          313.000000                          313.000000   
mean                             0.475801                            0.329674   
std                              0.309408                            0.310695   
min                              0.031321                            0.000167   
25%                              0.217560                            0.056210   
50%                              0.450268                            0.225854   
75%                              0.766451                            0.577899   
max                              0.991295                            0.991295   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                          313.000000                 313.000000   
mean                             0.009151                   0.040503   
std                              0.414075                   0.523195   
min                             -1.213489                  -1.946036   
25%                             -0.271211                  -0.272569   
50%                              0.004742                   0.114310   
75%                              0.295807                   0.416697   
max                              1.026332                   1.070422   

       Integrated mean (Stage IV)  
count                  313.000000  
mean                     0.049654  
std                      0.589176  
min                     -1.670327  
25%                     -0.406809  
50%                      0.084735  
75%                      0.508628  
max                      1.350353  	
--------------------------------------------------------------------------------
TMDE Integrated mean (Stage I): NOT normally distributed
TMDE Integrated mean (Stage IV): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                            803.000000   
mean                             264.325031   
std                               72.127279   
min                               26.000000   
25%                              213.500000   
50%                              273.000000   
75%                              319.500000   
max                              407.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                          803.000000                          803.000000   
mean                             0.379887                            0.276214   
std                              0.300685                            0.293534   
min                              0.011885                            0.000015   
25%                              0.104845                            0.026766   
50%                              0.288801                            0.146738   
75%                              0.633648                            0.478195   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                          803.000000                 803.000000   
mean                             0.150585                  -0.098934   
std                              0.439283                   0.661758   
min                             -1.400211                  -1.670519   
25%                             -0.079990                  -0.558005   
50%                              0.195591                  -0.150044   
75%                              0.453088                   0.283065   
max                              1.540403                   2.222142   

       Integrated mean (Stage IV)  
count                  803.000000  
mean                     0.051651  
std                      0.755580  
min                     -2.059430  
25%                     -0.498856  
50%                      0.015582  
75%                      0.557861  
max                      2.406906  	
--------------------------------------------------------------------------------
TMDS Integrated mean (Stage I): NOT normally distributed
TMDS Integrated mean (Stage IV): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                            539.000000   
mean                             243.410019   
std                               76.983274   
min                               35.000000   
25%                              185.000000   
50%                              243.000000   
75%                              301.000000   
max                              434.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                          539.000000                          539.000000   
mean                             0.451343                            0.319258   
std                              0.318804                            0.311294   
min                              0.002894                            0.000005   
25%                              0.125234                            0.031599   
50%                              0.431203                            0.217601   
75%                              0.743869                            0.563077   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                          539.000000                 539.000000   
mean                             0.097568                   0.029103   
std                              0.650350                   0.707442   
min                             -1.756362                  -2.393419   
25%                             -0.315861                  -0.396441   
50%                              0.090446                   0.086172   
75%                              0.526084                   0.546539   
max                              2.348416                   1.727148   

       Integrated mean (Stage IV)  
count                  539.000000  
mean                     0.126671  
std                      0.659368  
min                     -1.920737  
25%                     -0.261310  
50%                      0.132369  
75%                      0.560335  
max                      2.173560  	
--------------------------------------------------------------------------------
TPDS Integrated mean (Stage I): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                            415.000000   
mean                             242.698795   
std                               68.073691   
min                               48.000000   
25%                              203.000000   
50%                              242.000000   
75%                              295.500000   
max                              396.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                          415.000000                          415.000000   
mean                             0.557452                            0.375550   
std                              0.327268                            0.328739   
min                              0.033074                            0.000117   
25%                              0.250505                            0.065192   
50%                              0.592764                            0.299953   
75%                              0.883297                            0.670454   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                          415.000000                 415.000000   
mean                            -0.100960                  -0.091979   
std                              0.371756                   0.379639   
min                             -1.265367                  -1.499038   
25%                             -0.338354                  -0.298234   
50%                             -0.087780                  -0.054614   
75%                              0.113342                   0.148468   
max                              1.504833                   1.065135   

       Integrated mean (Stage IV)  
count                  415.000000  
mean                    -0.192938  
std                      0.413432  
min                     -1.632167  
25%                     -0.446952  
50%                     -0.172830  
75%                      0.066966  
max                      1.084019  	
--------------------------------------------------------------------------------
MDE Integrated mean (Stage I): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                            257.000000   
mean                             211.101167   
std                               78.029726   
min                               46.000000   
25%                              156.000000   
50%                              212.000000   
75%                              263.000000   
max                              388.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                          257.000000                          257.000000   
mean                             0.457742                            0.326464   
std                              0.332162                            0.316661   
min                              0.010055                            0.000098   
25%                              0.123045                            0.031599   
50%                              0.433516                            0.217601   
75%                              0.789513                            0.592903   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                          257.000000                 257.000000   
mean                            -0.085753                  -0.029664   
std                              0.516294                   0.471243   
min                             -1.440475                  -1.615232   
25%                             -0.410730                  -0.269684   
50%                             -0.030469                  -0.011915   
75%                              0.213879                   0.265253   
max                              1.208606                   1.332875   

       Integrated mean (Stage IV)  
count                  257.000000  
mean                    -0.115417  
std                      0.496198  
min                     -1.581586  
25%                     -0.453445  
50%                     -0.066505  
75%                      0.245156  
max                      1.092725  	
--------------------------------------------------------------------------------
TPDE Integrated mean (Stage I): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                           1308.000000   
mean                             229.801223   
std                               76.518018   
min                               28.000000   
25%                              179.000000   
50%                              232.000000   
75%                              286.000000   
max                              416.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                         1308.000000                         1308.000000   
mean                             0.490236                            0.339809   
std                              0.320967                            0.313715   
min                              0.007520                            0.000018   
25%                              0.189651                            0.048283   
50%                              0.498549                            0.251943   
75%                              0.786529                            0.592903   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                         1308.000000                1308.000000   
mean                             0.013684                   0.577703   
std                              0.271272                   0.992113   
min                             -0.862521                  -0.938056   
25%                             -0.147468                  -0.152384   
50%                              0.011868                   0.244758   
75%                              0.183795                   1.494527   
max                              1.007886                   3.572372   

       Integrated mean (Stage IV)  
count                 1308.000000  
mean                     0.591386  
std                      1.038351  
min                     -0.837347  
25%                     -0.128703  
50%                      0.206461  
75%                      1.492658  
max                      3.636135  	
--------------------------------------------------------------------------------
MDE_TMDS Integrated mean (Stage I): NOT normally distributed
MDE_TMDS Integrated mean (Stage IV): NOT normally distributed
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                            131.000000   
mean                             189.206107   
std                               72.628636   
min                               16.000000   
25%                              134.500000   
50%                              181.000000   
75%                              234.000000   
max                              387.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                          131.000000                          131.000000   
mean                             0.412236                            0.299179   
std                              0.321507                            0.315091   
min                              0.000703                            0.000005   
25%                              0.113796                            0.029106   
50%                              0.329174                            0.165844   
75%                              0.636040                            0.478300   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                          131.000000                 131.000000   
mean                            -0.262702                   0.147673   
std                              0.473466                   0.622853   
min                             -1.625160                  -1.621239   
25%                             -0.594743                  -0.172941   
50%                             -0.263300                   0.171570   
75%                              0.060156                   0.550868   
max                              1.131278                   1.392005   

       Integrated mean (Stage IV)  
count                  131.000000  
mean                    -0.115029  
std                      0.514944  
min                     -1.635124  
25%                     -0.399274  
50%                     -0.089361  
75%                      0.190053  
max                      1.092992  	
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Summary
	Cond1: 10 vs Cond0: 45
	       mannwhitneyu stat (Stage IV-Stage I)  \
count                            463.000000   
mean                             188.365011   
std                               70.457923   
min                                9.000000   
25%                              135.000000   
50%                              186.000000   
75%                              238.500000   
max                              398.000000   

       Integrated padj (Stage IV-Stage I)  Integrated pval (Stage IV-Stage I)  \
count                          463.000000                          463.000000   
mean                             0.431394                            0.306698   
std                              0.310910                            0.303573   
min                              0.001189                            0.000003   
25%                              0.148533                            0.038177   
50%                              0.387465                            0.194151   
75%                              0.719006                            0.541217   
max                              1.000000                            1.000000   

       Integrated diff (Stage IV-Stage I)  Integrated mean (Stage I)  \
count                          463.000000                 463.000000   
mean                            -0.206640                   0.122165   
std                              0.327343                   0.747753   
min                             -1.526980                  -1.700895   
25%                             -0.400839                  -0.351986   
50%                             -0.176619                  -0.054734   
75%                              0.018289                   0.254284   
max                              0.792915                   2.052425   

       Integrated mean (Stage IV)  
count                  463.000000  
mean                    -0.084475  
std                      0.843808  
min                     -1.813267  
25%                     -0.628469  
50%                     -0.292154  
75%                      0.093517  
max                      2.085422  	
--------------------------------------------------------------------------------
MDS_TMDE Integrated mean (Stage I): NOT normally distributed
MDS_TMDE Integrated mean (Stage IV): NOT normally distributed
Out[8]:
id mannwhitneyu stat (Stage IV-Stage I) Integrated padj (Stage IV-Stage I) Integrated pval (Stage IV-Stage I) Integrated diff (Stage IV-Stage I) Integrated mean (Stage I) Integrated mean (Stage IV) Stage I_C3L.01352 Stage I_C3L.01836 Stage I_C3N.01261 ... Regulation_Grouping_2 Protein-LogFC mean (Stage IV) Protein-LogFC mean (Stage I) Protein-LogFC mean (Stage IV-Stage I) RNA-LogFC mean (Stage IV) RNA-LogFC mean (Stage I) RNA-LogFC mean (Stage IV-Stage I) CpG-LogFC mean (Stage IV) CpG-LogFC mean (Stage I) CpG-LogFC mean (Stage IV-Stage I)
0 ENSG00000000005 190.0 0.695429 0.451539 -0.073670 0.125192 0.051522 0.379473 0.324155 -0.044577 ... TPDS_TMDE 0.000000 0.000000 0.000000 -0.821786 -0.617844 -0.203942 -0.434079 -0.305547 -0.128532
1 ENSG00000003096 226.0 0.995501 0.991295 -0.005227 1.350647 1.345420 1.264048 1.396797 1.356239 ... TPDS_TMDE -0.417617 -0.283684 -0.133933 -2.241165 -2.058036 -0.183129 -0.067677 -0.079235 0.011559
2 ENSG00000004939 119.0 0.142160 0.021324 -0.189416 1.255321 1.065905 1.065281 1.134694 1.345614 ... TPDS_TMDE 1.394054 1.466043 -0.071989 -5.000432 -5.672828 0.672396 -0.141396 -0.121519 -0.019877
3 ENSG00000005001 137.0 0.238975 0.056210 -0.302341 -0.638235 -0.940576 -0.788824 -0.499663 -0.610327 ... TPDS_TMDE 0.000000 0.000000 0.000000 -2.522605 -1.952379 -0.570226 -0.168012 -0.157581 -0.010431
4 ENSG00000006071 256.0 0.733482 0.505689 0.062979 -0.167911 -0.104932 0.432397 -0.208250 0.374605 ... TPDS_TMDE 0.000000 0.000000 0.000000 -0.294600 -0.492712 0.198112 -0.096770 -0.145593 0.048824
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
458 ENSG00000273045 339.0 0.078696 0.013258 0.314148 1.160627 1.474775 1.130754 0.924780 1.098500 ... MDS_TMDE -0.261270 -0.321215 0.059944 -0.859941 -0.989851 0.129910 0.219305 0.150133 0.069172
459 ENSG00000273274 168.0 0.412908 0.217601 -0.280006 0.030177 -0.249829 0.161288 0.213268 -0.401922 ... MDS_TMDE 0.000000 0.000000 0.000000 -0.208227 -0.450848 0.242621 0.169898 0.066255 0.103642
460 ENSG00000273328 187.0 0.617099 0.413176 -0.159038 -0.164170 -0.323208 0.047819 -0.272623 0.125869 ... MDS_TMDE 0.000000 0.000000 0.000000 -0.739841 -0.769299 0.029459 0.232026 0.166405 0.065622
461 ENSG00000277893 201.0 0.769241 0.608083 -0.061593 -0.515018 -0.576611 0.401482 -0.959410 -0.931824 ... MDS_TMDE 0.000000 0.000000 0.000000 -0.350238 -0.963343 0.613105 0.297978 0.173261 0.124717
462 ENSG00000278535 115.0 0.087772 0.016872 -0.325118 0.134856 -0.190262 -0.339662 0.509200 -0.036737 ... MDS_TMDE 0.000000 0.000000 0.000000 -1.764170 -1.722344 -0.041827 0.138939 0.084016 0.054923

6718 rows × 72 columns

Compile statistics information and compute GSEA for each comparison¶

In [9]:
import os
from scipy import stats
from tqdm import tqdm
from scipy.stats import combine_pvalues

save_df = True

files = os.listdir(stats_vae_dir)
stats_files = [f for f in files if 'stats' in f]

rcm_labels = ["MDS", "MDS_TMDE", "MDE", "MDE_TMDS", "TMDE", "TMDS", "TPDE", "TPDE_TMDS",  "TPDS", "TPDS_TMDE"]
stats_summary = [] # rows
summary_df = pd.DataFrame(columns=['Regulatory_cluster'])

# Go Through both
comparisons = ['old-young', 'PBRM1-BAP1', 'Stage IV-Stage I']

vae_rcm_df = meta_rcm_df.copy() # Make a copy that we'll add to

for comp in comparisons:
    all_dfs = pd.DataFrame()
    cond0 = comp.split('-')[1]
    cond1 =  comp.split('-')[0]
    tag = f'{cond1}-{cond0}'
    for f in tqdm(stats_files):
        if label in f and cond0 in f and cond1 in f and 'stats' in f:
            df = pd.read_csv(f'{stats_vae_dir}{f}', index_col=0)
            df.set_index('id', inplace=True)
            df_merged = df.join(vae_rcm_df, how='left', lsuffix='_')  # Join to the 
            # Map gene names and move folder
            df_merged = df_merged[['external_gene_name', 
                                   'Regulation_Grouping_2', 
                                   f'Integrated padj ({cond1}-{cond0})',
                                   f'Integrated pval ({cond1}-{cond0})', 
                                   f'Integrated diff ({cond1}-{cond0})', 
                                   f'mannwhitneyu stat ({cond1}-{cond0})',
                                   f'Integrated mean ({cond0})', 
                                   f'Integrated mean ({cond1})',
                                   f'Protein-LogFC mean ({cond1}-{cond0})', 
                                   f'RNA-LogFC mean ({cond1}-{cond0})',
                                   f'CpG-LogFC mean ({cond1}-{cond0})',
                                   'hgnc_symbol',
                                   'entrezgene_id',
                                   'logFC_rna', 
                                   'padj_rna',
                                   'CpG_Beta_diff', 
                                   'padj_meth', 
                                   'logFC_protein', 
                                   'padj_protein']] # Reorder columns
            df_merged.to_csv(f'{stats_output_dir}{missing_method}_Integrated_comparison_{cond1}-{cond0}.csv')
            for c in df_merged.columns:
                if 'Integrated diff' in c or 'Integrated padj' in c or 'mean' in c:
                        vae_rcm_df.loc[df_merged.index.values, c] = df_merged[c].values
                        

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Plot the correlations as a QC to ensure it is logical/interpretable¶

In [10]:
diff_df = vae_rcm_df[[c for c in vae_rcm_df if ' diff' in c or 'LogFC' in c]]
corr = diff_df.corr()
sns.clustermap(corr, 
            xticklabels=corr.columns.values,
            yticklabels=corr.columns.values, cmap='RdBu_r', row_cluster=True, col_cluster=True)
if save_fig:
    plt.savefig(f'{stats_fig_dir}{missing_method}_VAE_data_corr.svg', transparent=True)

Check decoding of some of the top genes¶

Again, check everything has been learnt "correctly" by ensuring the decoding looks like the input somewhat

In [11]:
from sciviso import Scatterplot
import matplotlib.pyplot as plt

rcm_labels = ["MDS", "TPDS", "TMDS", 
              "MDE", "TPDE", "TMDE", 
              "MDS_TMDE", "MDE_TMDS", "TPDE_TMDS", "TPDS_TMDE"]

p_cutoff = 0.05

for comparison in comparisons:
    fig, axs = plt.subplots(10, 3, figsize=(6,21))
    vae_change = f'Integrated diff ({comparison})'
    vae_p = f'Integrated padj ({comparison})'

    protein_change = f'Protein-LogFC mean ({comparison})'
    rna_change = f'RNA-LogFC mean ({comparison})'
    cpg_change = f'CpG-LogFC mean ({comparison})'
    
    for fi, r in enumerate(rcm_labels):
        tmp_df = vae_rcm_df[vae_rcm_df['Regulation_Grouping_2'] == r]

        opts = {'title_font_weight': 'bold', "title_font_size":9, "label_font_size":7, "figsize": (6, 9), "s": 20}
        corr_c = round(np.corrcoef(tmp_df[vae_change], tmp_df[cpg_change])[0][1], 2)
        scatter = Scatterplot(tmp_df, vae_change, cpg_change,
                              title_font_weight="bold",
                              colour='orange', config=opts)
        grp_labels = ['Integrated']
        vae_sig = []
        vae_int_change = abs(tmp_df[vae_change].values)
        vae_cutoff = 0.5
        for i, vae_padj in enumerate(tmp_df[vae_p].values):
            if (vae_padj < p_cutoff and vae_int_change[i] > vae_cutoff):
                vae_sig.append(i)
        grp_idxs = [vae_sig]
        print(r, len(vae_sig)/len(tmp_df))
        
        ax = scatter.plot_groups_2D(axs[fi][0], grp_labels, grp_idxs, ['orange'])

        corr_r = round(np.corrcoef(tmp_df[vae_change], tmp_df[rna_change])[0][1], 2)
        scatter = Scatterplot(tmp_df, vae_change, rna_change,  colour='rebeccapurple',
                              xlabel='Integrated Rank (Stage 4 - Stage 1)',
                               config=opts)
        ax = scatter.plot_groups_2D(axs[fi][1], grp_labels, grp_idxs, ['orange', 'rebeccapurple', 'darkred'])

        corr_p = round(np.corrcoef(tmp_df[vae_change], tmp_df[protein_change])[0][1], 2)
        scatter = Scatterplot(tmp_df, vae_change, protein_change, colour='grey',
                             config=opts)
        ax = scatter.plot_groups_2D(axs[fi][2], grp_labels, grp_idxs, ['orange', 'rebeccapurple', 'darkred'])
        plt.tight_layout()

        axs[fi][0].set_title(f'CpG ({corr_c})', fontweight="bold")
        axs[fi][1].set_title(f'{r} \n \n RNA ({corr_r})',  fontweight="bold")
        axs[fi][2].set_title(f'Protein ({corr_p})', fontweight="bold")
        
        axs[fi][0].set(xlabel='Integrated diff', ylabel='CpG diff')
        axs[fi][1].set(xlabel='Integrated diff', ylabel='RNA LogFC')
        axs[fi][2].set(xlabel='Integrated diff', ylabel='Protein LogFC')

    if save_fig:
        plt.savefig(f'{stats_fig_dir}{missing_method}_VAE_data_corr_{comparison}_change.svg', transparent=True)
    plt.show()

MDS 0.0
TPDS 0.0
TMDS 0.037359900373599
MDE 0.0
TPDE 0.019455252918287938
TMDE 0.0
MDS_TMDE 0.0
MDE_TMDS 0.0
TPDE_TMDS 0.0
TPDS_TMDE 0.0

MDS 0.09923664122137404
TPDS 0.09461966604823747
TMDS 0.05977584059775841
MDE 0.04819277108433735
TPDE 0.11673151750972763
TMDE 0.0670926517571885
MDS_TMDE 0.01511879049676026
MDE_TMDS 0.02522935779816514
TPDE_TMDS 0.02432179607109448
TPDS_TMDE 0.015492957746478873

MDS 0.06870229007633588
TPDS 0.10946196660482375
TMDS 0.10585305105853052
MDE 0.05060240963855422
TPDE 0.14396887159533073
TMDE 0.07348242811501597
MDS_TMDE 0.09071274298056156
MDE_TMDS 0.052752293577981654
TPDE_TMDS 0.025257249766136577
TPDS_TMDE 0.03169014084507042
In [12]:
from sciviso import Scatterplot
import matplotlib.pyplot as plt

rcm_labels = ["MDS", "TPDS", "TMDS", 
              "MDE", "TPDE", "TMDE", 
              "MDS_TMDE", "MDE_TMDS", "TPDE_TMDS", "TPDS_TMDE"]

p_cutoff = 0.05

for comparison in comparisons:
    fig, axs = plt.subplots(10, 2, figsize=(4,24))
    cond0 = comparison.split('-')[1]
    cond1 =  comparison.split('-')[0]    
    vae_change = f'Integrated mean ({cond0})'

    for fi, r in enumerate(rcm_labels):
        tmp_df = vae_rcm_df[vae_rcm_df['Regulation_Grouping_2'] == r]

        axs[fi][0].hist(tmp_df[f'Integrated diff ({comparison})'], color='orange')

        axs[fi][1].hist(tmp_df[f'Integrated mean ({cond0})'], color='blue', alpha=0.2)
        axs[fi][1].hist(tmp_df[f'Integrated mean ({cond1})'], color='red', alpha=0.2)
        axs[fi][1].set_title(r)
    if save_fig:
        plt.savefig(f'{stats_fig_dir}{missing_method}_VAE_hists_{comparison}_change.svg', transparent=True)
    plt.show()
In [13]:
# get the gene ids that we're interested in visualising
#from sciviso import Heatmap
import scipy.spatial as sp, scipy.cluster.hierarchy as hc
r = 'MDS'
cond1 = 'Stage IV'
cond0 = 'Stage I'

comparison = f'{cond1}-{cond0}'
vae_diff = f'Integrated diff ({comparison})'
vae_padj = f'Integrated padj ({comparison})'

protein_change = f'Protein-LogFC mean ({comparison})'
rna_change = f'RNA-LogFC mean ({comparison})'
cpg_change = f'CpG-LogFC mean ({comparison})'
    
# Read in the precomputed encoding and decoding dfs
decoding_df = sv.get_decoding(r)
training_df = sv.vae_input_df[r] # Get the input DF

r_df = pd.read_csv(f'{stats_output_dir}{label}_Integrated_comparison_{cond1}-{cond0}.csv')
r_df = r_df[r_df['Regulation_Grouping_2'] == r]

training_df
# Get the highest 5 pvalues as a control
worst_gene_ids = r_df.nlargest(10, vae_padj)['id'].values
row_colours = ['black'] * len(worst_gene_ids)

# Get the nlargest and nsmallest values from the integrated value
r_df = r_df[r_df[vae_padj] <= 0.05]
# Get the top and bottom
r_df = r_df[abs(r_df[vae_diff]) > 0.5]

top_gene_ids = list(r_df[r_df[vae_diff] > 0]['id'].values)
top_gene_ids += list(r_df[r_df[vae_diff] < 0]['id'].values)
gene_colour = {}
for g in list(r_df[r_df[vae_diff] < 0]['id'].values):
    gene_colour[g] = 'purple'
    
for g in list(r_df[r_df[vae_diff] > 0]['id'].values):
    gene_colour[g] = 'yellow'
    
for g in worst_gene_ids:
    gene_colour[g] = 'white'
    
top_gene_ids += list(worst_gene_ids)
# Now we want to plot the top and bottom genes
# Plot genes from both
# Get top genes by encoding
feature_columns = ['Protein', 'RNA', 'CpG'] 
training_df = training_df.join(vae_rcm_df, how='left', lsuffix='_', rsuffix='_r')
plot_df = training_df[training_df.index.isin(top_gene_ids)]  
decoding_df.set_index('id', inplace=True)
# Do the same for decoding
decoding_df = decoding_df.join(vae_rcm_df, how='left', lsuffix='_', rsuffix='_r')
plot_dec_df = decoding_df[decoding_df.index.isin(top_gene_ids)]  

row_colours = []
for g in plot_dec_df.index.values:
    row_colours.append(gene_colour.get(g))
    
fig_size = (8, 10)
vis_opts = {"figsize": fig_size, "title_font_size": 12, "axis_font_size": 10}

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Validation and supplemental figures.¶

We want to do some validation and QC plots for each of the comparisons.

  1. Correlation heatmap with VAE results and the raw data. (across all clusters)
  2. Correlation scatterplot of the VAE compared with the main logFC. (for specific clusters)
  3. boxplots for the top an dbottmo 5 genes within each cluster (coloured by the patient features)
In [14]:
cond0_cases = list(patient_info[patient_info['TumorStage'] == cond0]['SafeCases'].values)
cond1_cases = list(patient_info[patient_info['TumorStage'] == cond1]['SafeCases'].values)
In [15]:
from sciviso import Heatmap
# get the genes that chanegd the mosy between
for f in feature_columns:
    try:
        s1_f_cols = [c for c in training_df.columns if f in c and 'Normal' in c and c.split('_')[0] in cond0_cases]
        s4_f_cols = [c for c in training_df.columns if f in c and 'Normal' in c and c.split('_')[0] in cond1_cases]

        s1_f_cols_t = [c for c in training_df.columns if f in c and 'Tumor' in c and c.split('_')[0] in cond0_cases]
        s4_f_cols_t = [c for c in training_df.columns if f in c and 'Tumor' in c and c.split('_')[0] in cond1_cases]

        column_colours_TN = ['blue'] * len(s1_f_cols) + ['orange'] * len(s1_f_cols_t) + ['cyan'] * len(s4_f_cols) + ['red'] * len(s4_f_cols_t)

        s1_f_cols = s1_f_cols + s1_f_cols_t
        s4_f_cols = s4_f_cols + s4_f_cols_t

        train_columns = s1_f_cols + s4_f_cols
        train_columns = [c for c in train_columns if c in plot_dec_df.columns]
        column_colours = ['green'] * len(s1_f_cols) + ['pink'] * len(s4_f_cols)
        # Combine the two dfs 
        # Pre compute the distance 
        vals = plot_df[train_columns]
        if len(vals) > 0:
            row_linkage, col_linkage = (hc.linkage(sp.distance.pdist(x), method='average')
                for x in (vals.values, vals.values.T))

            hm = Heatmap(plot_df, row_index='hgnc_symbol', 
                         chart_columns=train_columns, #cluster_cols=False, cluster_rows=False,
                         col_colours=[column_colours, column_colours_TN], row_colours=[row_colours],
                        config=vis_opts, title=f'{r} {f} training')
            hm.axis_line_width = 1.0
            hm.plot(row_linkage=row_linkage, col_linkage=col_linkage)
            plt.show()



            hm = Heatmap(plot_dec_df, row_index='hgnc_symbol', 
                         col_colours=[column_colours, column_colours_TN],  row_colours=[row_colours],
                         chart_columns=train_columns, #cluster_cols=False,cluster_rows=False,
                        config=vis_opts, title=f'{r} {f} decoding')
            hm.axis_line_width = 1.0
            hm.plot(row_linkage=row_linkage, col_linkage=col_linkage)
            plt.show()
    except:
        print(f)

CpG
In [16]:
f = 'CpG'

train_columns = [c for c in training_df.columns if '_CpG-LogFC' in c] #s1_f_cols + s4_f_cols
train_columns = [c for c in train_columns if c in plot_dec_df.columns]
# Combine the two dfs 
# Pre compute the distance 
vals = plot_df[train_columns]
if len(vals) > 0:
    row_linkage, col_linkage = (hc.linkage(sp.distance.pdist(x), method='average')
        for x in (vals.values, vals.values.T))

    hm = Heatmap(plot_df, row_index='hgnc_symbol', 
                 chart_columns=train_columns, #cluster_cols=False, cluster_rows=False,
                 col_colours=[column_colours, column_colours_TN], row_colours=[row_colours],
                config=vis_opts, title=f'{r} {f} training')
    hm.axis_line_width = 1.0
    hm.plot(row_linkage=row_linkage, col_linkage=col_linkage)
    plt.show()



    hm = Heatmap(plot_dec_df, row_index='hgnc_symbol', 
                 col_colours=[column_colours, column_colours_TN],  row_colours=[row_colours],
                 chart_columns=train_columns, #cluster_cols=False,cluster_rows=False,
                config=vis_opts, title=f'{r} {f} decoding')
    hm.axis_line_width = 1.0
    hm.plot(row_linkage=row_linkage, col_linkage=col_linkage)
    plt.show()

Plot some of the top genes in each group and colour by the¶

Do box plots of specific genes¶

In [17]:
ens_to_gene = dict(zip(vae_rcm_df.index.values, vae_rcm_df['external_gene_name'].values))
values = defaultdict(lambda: defaultdict(list))
for r in rcm_labels:
    encoding_df = sv.encoded_df[r]
    input_df = sv.raw_input_df[r] # Get the input DF
    # Make a df for each of the data types we want box plots for 
    for column in input_df.columns:
        if 'C' in column:
            c = column.split('_')
            values[c[1]]['values'] += [v for v in input_df[column].values]
            values[c[1]]['GeneId'] += [v for v in input_df.index.values]
            values[c[1]]['Cluster'] += [v for v in input_df['Regulation_Grouping_2'].values]
            case_info = patient_info[patient_info['SafeCases'] == c[0]]
            # Stage	BAP1&PBRM1 gender	TumorStage	AgeGrouped
            values[c[1]]['Gender'] += [case_info['gender'].values[0]] * len(input_df)
            values[c[1]]['Stage'] += [case_info['Stage'].values[0]] * len(input_df)
            values[c[1]]['Tumor Stage'] += [case_info['TumorStage'].values[0]] * len(input_df)
            values[c[1]]['Age'] += [case_info['AgeGrouped'].values[0]] * len(input_df)
            values[c[1]]['Mutation'] += [case_info['BAP1&PBRM1'].values[0]] * len(input_df)
            
    # Now we also want an encoding values 
    for column in encoding_df.columns:
        if 'C' in column:
            values['Integrated']['values'] += [c for c in encoding_df[column].values]
            values['Integrated']['GeneId'] += [c for c in encoding_df['id'].values]
            values['Integrated']['Cluster'] += [v for v in encoding_df['Regulation_Grouping_2'].values]
            case_info = patient_info[patient_info['SafeCases'] == column]

            values['Integrated']['Gender'] += [case_info['gender'].values[0]] * len(encoding_df)
            values['Integrated']['Stage'] += [case_info['Stage'].values[0]] * len(encoding_df)
            values['Integrated']['Tumor Stage'] += [case_info['TumorStage'].values[0]] * len(encoding_df)
            values['Integrated']['Age'] += [case_info['AgeGrouped'].values[0]] * len(encoding_df)
            values['Integrated']['Mutation'] += [case_info['BAP1&PBRM1'].values[0]] * len(encoding_df)
In [18]:
# Just formatting the data for a boxplot
dfs = {}
for v in values:
    print(v)
    box_df = pd.DataFrame()
    for c in values[v]:
        box_df[c] = values[v][c]
    dfs[v] = box_df
    
for d in dfs:
    dfs[d].to_csv(f'{stats_base_dir}Boxplot_data_{d}.csv', index=False)

Protein-Normal
Protein-Tumor
Protein-LogFC
RNA-Normal
RNA-Tumor
RNA-LogFC
CpG-Normal
CpG-Tumor
CpG-LogFC
Integrated

Plotting function for a gene across the data types¶

In [19]:
# Now we can iterate through each one and do whatever we need to do
plt.rcParams["figure.figsize"] = (12, 3)
plt.rcParams['svg.fonttype'] = 'none' 
import os
from sciviso import Boxplot

fig_size = (12, 3)
vis_opts = {"figsize": fig_size, "title_font_size": 12, "axis_font_size": 10, 
           'palette': ['lightgrey', 'dimgrey']}

def plot_gene_logfcs(gene, cond0, cond1, x="Stage", cmap="Purples"):
    fig, ax = plt.subplots(nrows=1, ncols=5)
    gene_name = ens_to_gene.get(gene)
    box_data_df = dfs['Integrated']
    #try:
    
    box_data_df = box_data_df[box_data_df[x].isin([cond0, cond1])]
    gene_data = box_data_df[box_data_df['GeneId'] == gene]
    b = Boxplot(gene_data, x=x, y="values",  add_dots=True, 
            add_stats=True, title=f'Integrated diff.',
            xlabel="Sample", ylabel=f'diff. {cond1}-{cond0}', config=vis_opts)
    b.plot(ax=ax[0], legend=False)
    #nt('Integrated')
    
    box_data_df = dfs['Protein-LogFC']
    try:
        box_data_df = box_data_df[box_data_df[x].isin([cond0, cond1])]
        gene_data = box_data_df[box_data_df['GeneId'] == gene]
        b = Boxplot(gene_data, x=x, y="values", add_dots=True, 
                add_stats=True, title=f'Protein logFC',
                xlabel="Sample", ylabel=f"Protein  {cond1}-{cond0}", config=vis_opts)
        b.plot(ax=ax[1])
    except:
        print('Protein logFC')
        
    box_data_df = dfs['Protein-Tumor']
    try:
        box_data_df = box_data_df[box_data_df[x].isin([cond0, cond1])]
        gene_data = box_data_df[box_data_df['GeneId'] == gene]
        b = Boxplot(gene_data, x=x, y="values", add_dots=True, 
                add_stats=True, title=f'Protein Tumor',
                xlabel="Sample", ylabel=f"Protein  {cond1}-{cond0}", config=vis_opts)
        b.plot(ax=ax[2])
    except:
        print('Protein')
        
    box_data_df = dfs['RNA-LogFC']
    try:
        box_data_df = box_data_df[box_data_df[x].isin([cond0, cond1])]
        gene_data = box_data_df[box_data_df['GeneId'] == gene]
        b = Boxplot(gene_data, x=x, y="values", add_dots=True, 
                add_stats=True, title=f'RNA logFC',
                xlabel="Sample", ylabel=f"RNA {cond1}-{cond0}", config=vis_opts)
        b.plot(ax=ax[3])
    except:
        print('RNA')
    box_data_df = dfs['CpG-LogFC']
    try:
        box_data_df = box_data_df[box_data_df[x].isin([cond0, cond1])]
        gene_data = box_data_df[box_data_df['GeneId'] == gene]
        
        b = Boxplot(gene_data, x=x, y="values", add_dots=True, 
                add_stats=True, title=f'CpG logFC',
                xlabel="Sample", ylabel=f"CpG {cond1}-{cond0}", config=vis_opts)
        b.plot(ax=ax[4])
    except:
        print('CpG')
    # ALso print the URL so that I can quickly check the ones that look good in protein atlas
    print(f'https://www.proteinatlas.org/{gene}-{gene_name}/pathology/renal+cancer/KIRC')
    fig.suptitle(f'{gene_name} ({cond1}-{cond0})', fontsize=16, fontweight='bold')
    fig.tight_layout()
    fig.subplots_adjust(top=0.8)
    if save_fig:
        plt.savefig(f'{fig_dir}boxplot_{gene_name}_{cond1}-{cond0}.svg')
    plt.show()
In [20]:
gene_to_ens = dict(zip(vae_rcm_df['external_gene_name'].values, vae_rcm_df.index.values))
ens_to_gene = dict(zip(vae_rcm_df.index.values, vae_rcm_df.external_gene_name.values))
for gene_name in ['FLT1', 'EPAS1', 'LGALS9', 'HIF1A', 'SLC3A1']:
    plot_gene_logfcs(gene_to_ens[gene_name], 'BAP1', 'PBRM1',  x='Mutation')
    # Do the same for old and young
    plot_gene_logfcs(gene_to_ens[gene_name], 'young', 'old',  x='Age')
    # And stage
    plot_gene_logfcs(gene_to_ens[gene_name], 'Stage I', 'Stage IV',  x='Tumor Stage')

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.311e-04 U_stat=7.700e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.158e-01 U_stat=1.840e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.082e-02 U_stat=1.490e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.956e-04 U_stat=7.900e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.850e-02 U_stat=3.250e+02
https://www.proteinatlas.org/ENSG00000102755-FLT1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.088e-01 U_stat=2.870e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.844e-01 U_stat=3.210e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.432e-01 U_stat=2.820e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.998e-01 U_stat=2.760e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.590e-01 U_stat=1.650e+02
https://www.proteinatlas.org/ENSG00000102755-FLT1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.132e-02 U_stat=3.310e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.715e-01 U_stat=3.480e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.453e-02 U_stat=3.850e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.769e-02 U_stat=3.700e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.426e-01 U_stat=1.800e+02
https://www.proteinatlas.org/ENSG00000102755-FLT1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.176e-03 U_stat=8.100e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.987e-03 U_stat=1.120e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.049e-04 U_stat=9.800e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.222e-02 U_stat=1.190e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.064e-02 U_stat=3.380e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000116016-EPAS1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.921e-01 U_stat=2.230e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.391e-01 U_stat=3.010e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.296e-01 U_stat=3.310e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.246e-01 U_stat=2.200e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.446e-01 U_stat=2.290e+02
https://www.proteinatlas.org/ENSG00000116016-EPAS1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.391e-02 U_stat=3.290e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.604e-01 U_stat=3.050e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.228e-01 U_stat=2.340e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.913e-02 U_stat=3.690e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.053e-03 U_stat=1.060e+02
https://www.proteinatlas.org/ENSG00000116016-EPAS1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.470e-02 U_stat=1.140e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.450e-02 U_stat=3.440e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.511e-03 U_stat=3.910e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.955e-04 U_stat=3.840e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.278e-02 U_stat=1.320e+02
https://www.proteinatlas.org/ENSG00000168961-LGALS9/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.709e-03 U_stat=3.590e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.608e-01 U_stat=1.710e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.971e-01 U_stat=1.770e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.232e-03 U_stat=9.400e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.182e-01 U_stat=2.460e+02
https://www.proteinatlas.org/ENSG00000168961-LGALS9/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.700e-01 U_stat=2.330e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.796e-01 U_stat=3.470e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.084e-02 U_stat=1.960e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.583e-01 U_stat=2.680e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.036e-01 U_stat=3.340e+02
https://www.proteinatlas.org/ENSG00000168961-LGALS9/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.649e-03 U_stat=8.500e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.119e-01 U_stat=2.410e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.761e-02 U_stat=1.600e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.649e-03 U_stat=1.050e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.852e-02 U_stat=1.510e+02
https://www.proteinatlas.org/ENSG00000100644-HIF1A/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.314e-01 U_stat=1.750e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.497e-02 U_stat=1.440e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.748e-02 U_stat=1.450e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.180e-01 U_stat=1.800e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.431e-01 U_stat=2.730e+02
https://www.proteinatlas.org/ENSG00000100644-HIF1A/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.046e-03 U_stat=3.540e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.602e-05 U_stat=5.090e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.301e-02 U_stat=3.980e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.406e-03 U_stat=4.200e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.751e-02 U_stat=3.380e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000100644-HIF1A/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.747e-01 U_stat=2.380e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.367e-01 U_stat=3.300e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.478e-02 U_stat=3.750e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.261e-01 U_stat=2.320e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.666e-01 U_stat=3.080e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000138079-SLC3A1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.483e-01 U_stat=2.820e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.036e-01 U_stat=3.180e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.650e-01 U_stat=2.650e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.566e-01 U_stat=2.710e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

old v.s. young: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.711e-01 U_stat=1.810e+02
https://www.proteinatlas.org/ENSG00000138079-SLC3A1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.590e-02 U_stat=3.360e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.333e-01 U_stat=2.230e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.775e-01 U_stat=3.110e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.732e-02 U_stat=3.590e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.347e-02 U_stat=1.570e+02
https://www.proteinatlas.org/ENSG00000138079-SLC3A1/pathology/renal+cancer/KIRC
In [21]:
# Lastly, for a QC top ones done for each gene in the top/bottom 5 for each cluster.
# For each cluste pick the n largest and smallest and do teh above plots
rcm_labels = ["MDE", "TPDE", "TPDS", "TMDS", "TMDE", "MDS"]
from sciutil import SciUtil
u = SciUtil()
n = 5
comparisons = ['PBRM1-BAP1', 'Stage IV-Stage I', 'old-young']
labels = ['Mutation','Tumor Stage', 'Age']
for c_i, comparison in enumerate(comparisons):
    
    for r in rcm_labels:
        u.dp([r])
        r_df = vae_rcm_df[vae_rcm_df['Regulation_Grouping_2'] == r]
        # Filter to just significant
        vae_change = f'Integrated diff ({comparison})'
        vae_p = f'Integrated padj ({comparison})'
        cond1 = comparison.split('-')[0]
        cond0 = comparison.split('-')[1]

        r_df = r_df[r_df[vae_p] <= 0.05]

        top_df = r_df[r_df[vae_change] > 0]
        bot_df = r_df[r_df[vae_change] < 0]

        top_df = top_df.nlargest(n, vae_change)

        bot_df = bot_df.nsmallest(n, vae_change) 
        # For each of the IDs pop it through
        u.warn_p(['Top 5'])
        for ensembl_id in top_df.index.values:
            gene_name = ens_to_gene[ensembl_id] # Easier to use the gene name for display
            plot_gene_logfcs(ensembl_id, cond0, cond1, x=labels[c_i])
        u.warn_p(['Bottom 5'])
        for ensembl_id in bot_df.index.values:
            gene_name = ens_to_gene[ensembl_id] # Easier to use the gene name for display
            plot_gene_logfcs(ensembl_id, cond0, cond1, x=labels[c_i])

--------------------------------------------------------------------------------
                                      MDE	                                      
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                                     Top 5	                                     
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.049e-04 U_stat=3.740e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.987e-03 U_stat=1.120e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.189e-05 U_stat=5.100e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.180e-05 U_stat=4.400e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.898e-05 U_stat=4.270e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000185100-ADSS1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.742e-05 U_stat=3.840e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.500e-01 U_stat=2.040e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.909e-01 U_stat=2.660e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.372e-06 U_stat=3.600e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.157e-03 U_stat=3.750e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000132639-SNAP25/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.176e-03 U_stat=3.480e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.502e-04 U_stat=8.500e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.948e-04 U_stat=8.700e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.323e-03 U_stat=1.040e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.381e-01 U_stat=2.490e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000091127-PUS7/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.438e-05 U_stat=3.880e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.304e-04 U_stat=8.400e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.272e-06 U_stat=2.900e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.292e-04 U_stat=6.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.128e-02 U_stat=3.600e+02
https://www.proteinatlas.org/ENSG00000109107-ALDOC/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.822e-04 U_stat=3.560e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.721e-03 U_stat=1.360e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.039e-04 U_stat=9.600e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.604e-03 U_stat=9.100e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.330e-02 U_stat=3.480e+02
https://www.proteinatlas.org/ENSG00000024422-EHD2/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                   Bottom 5	                                    
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.576e-05 U_stat=5.300e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.758e-04 U_stat=4.280e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.799e-05 U_stat=4.500e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.435e-05 U_stat=4.150e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.316e-01 U_stat=2.610e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000198758-EPS8L3/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.261e-05 U_stat=3.500e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.189e-05 U_stat=4.670e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.065e-05 U_stat=4.570e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.967e-05 U_stat=4.080e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.788e-02 U_stat=3.280e+02
https://www.proteinatlas.org/ENSG00000277586-NEFL/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.994e-05 U_stat=5.100e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.208e-01 U_stat=3.330e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.927e-01 U_stat=2.920e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.113e-06 U_stat=4.290e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.128e-02 U_stat=3.270e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000075340-ADD2/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.281e-03 U_stat=8.200e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.960e-02 U_stat=3.570e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.217e-02 U_stat=3.610e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.465e-04 U_stat=3.770e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.031e-01 U_stat=2.390e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000242515-UGT1A10/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.356e-04 U_stat=6.700e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.502e-04 U_stat=4.330e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.573e-05 U_stat=4.470e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.031e-03 U_stat=3.610e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.733e-01 U_stat=2.950e+02
https://www.proteinatlas.org/ENSG00000105976-MET/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                     TPDE	                                      
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                                     Top 5	                                     
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.690e-06 U_stat=2.800e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.215e-04 U_stat=1.000e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.596e-06 U_stat=4.500e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.161e-05 U_stat=3.800e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.066e-01 U_stat=2.830e+02
https://www.proteinatlas.org/ENSG00000147231-RADX/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.758e-05 U_stat=3.800e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.300e-05 U_stat=6.700e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.270e-05 U_stat=7.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.043e-05 U_stat=3.700e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.483e-01 U_stat=2.600e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000147202-DIAPH2/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.656e-03 U_stat=9.800e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.367e-01 U_stat=1.880e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.968e-02 U_stat=1.480e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.597e-04 U_stat=7.600e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.909e-04 U_stat=4.030e+02
https://www.proteinatlas.org/ENSG00000079689-SCGN/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.918e-03 U_stat=9.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.836e-03 U_stat=1.250e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.022e-03 U_stat=1.180e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.583e-02 U_stat=1.230e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.733e-01 U_stat=2.950e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000087250-MT3/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.792e-03 U_stat=8.600e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.734e-01 U_stat=1.940e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.652e-01 U_stat=2.380e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.710e-04 U_stat=6.500e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000119630-PGF/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                   Bottom 5	                                    
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.691e-05 U_stat=3.800e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.685e-05 U_stat=4.550e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.919e-05 U_stat=4.620e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.701e-04 U_stat=3.850e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.446e-02 U_stat=3.560e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000177409-SAMD9L/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.822e-04 U_stat=3.560e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.511e-03 U_stat=3.910e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.612e-04 U_stat=4.190e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.558e-04 U_stat=3.910e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000012779-ALOX5/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.024e-03 U_stat=3.300e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.033e-02 U_stat=3.810e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.289e-03 U_stat=4.040e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.323e-03 U_stat=3.510e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000204632-HLA-G/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.486e-03 U_stat=3.390e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.142e-03 U_stat=3.830e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.314e-02 U_stat=3.770e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.481e-03 U_stat=3.650e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000157601-MX1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.649e-03 U_stat=3.440e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.196e-03 U_stat=4.130e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.022e-03 U_stat=4.000e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.640e-03 U_stat=3.450e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000128335-APOL2/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                     TPDS	                                      
--------------------------------------------------------------------------------
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                                     Top 5	                                     
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p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.162e-06 U_stat=3.000e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.455e-03 U_stat=1.150e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.065e-05 U_stat=6.100e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.595e-05 U_stat=4.100e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000165959-CLMN/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.964e-04 U_stat=7.500e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.585e-01 U_stat=2.150e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.566e-02 U_stat=1.440e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.292e-04 U_stat=6.200e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.559e-01 U_stat=2.480e+02
https://www.proteinatlas.org/ENSG00000175600-SUGCT/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.993e-03 U_stat=9.600e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.968e-02 U_stat=1.480e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.836e-03 U_stat=1.250e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.232e-04 U_stat=7.200e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.354e-01 U_stat=2.165e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000072042-RDH11/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.517e-03 U_stat=8.400e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.033e-02 U_stat=1.370e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.612e-04 U_stat=9.900e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.372e-03 U_stat=9.600e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.526e-01 U_stat=2.025e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000171723-GPHN/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.486e-03 U_stat=9.000e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.092e-01 U_stat=1.990e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.089e-02 U_stat=1.660e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.764e-03 U_stat=9.800e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.508e-01 U_stat=2.540e+02
https://www.proteinatlas.org/ENSG00000276644-DACH1/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                   Bottom 5	                                    
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.261e-05 U_stat=3.940e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.659e-02 U_stat=3.730e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.558e-04 U_stat=4.160e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.354e-04 U_stat=3.720e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.038e-01 U_stat=1.710e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000132855-ANGPTL3/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.261e-05 U_stat=3.940e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.511e-03 U_stat=3.910e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.722e-03 U_stat=4.080e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.771e-05 U_stat=4.130e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000167608-TMC4/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.160e-04 U_stat=3.730e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.659e-02 U_stat=3.730e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.602e-03 U_stat=4.090e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.419e-04 U_stat=3.920e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.822e-01 U_stat=2.260e+02
https://www.proteinatlas.org/ENSG00000154277-UCHL1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.684e-04 U_stat=3.610e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.287e-03 U_stat=4.120e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.277e-04 U_stat=4.410e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.465e-03 U_stat=3.540e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000118514-ALDH8A1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.365e-05 U_stat=3.850e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.879e-03 U_stat=3.900e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.163e-03 U_stat=3.920e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.771e-05 U_stat=4.130e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000135447-PPP1R1A/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                     TMDS	                                      
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                                     Top 5	                                     
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.055e-04 U_stat=6.600e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.061e-01 U_stat=2.270e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.167e-02 U_stat=1.620e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.826e-05 U_stat=5.800e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.136e-01 U_stat=1.730e+02
https://www.proteinatlas.org/ENSG00000072657-TRHDE/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.747e-05 U_stat=5.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.611e-02 U_stat=1.680e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.163e-03 U_stat=1.260e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.907e-05 U_stat=5.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.926e-02 U_stat=1.460e+02
https://www.proteinatlas.org/ENSG00000151338-MIPOL1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.176e-03 U_stat=8.100e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.527e-03 U_stat=1.240e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.455e-03 U_stat=1.150e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.261e-03 U_stat=8.800e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.185e-01 U_stat=2.220e+02
https://www.proteinatlas.org/ENSG00000172260-NEGR1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.041e-04 U_stat=6.900e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.264e-01 U_stat=2.120e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.110e-01 U_stat=1.830e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.980e-05 U_stat=5.400e+01
p-value annotation legend:

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.846e-02 U_stat=3.310e+02
https://www.proteinatlas.org/ENSG00000172828-CES3/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.964e-04 U_stat=7.500e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.697e-01 U_stat=2.160e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.542e-01 U_stat=1.910e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.597e-04 U_stat=7.600e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.822e-01 U_stat=2.260e+02
https://www.proteinatlas.org/ENSG00000257335-MGAM/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                   Bottom 5	                                    
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.311e-07 U_stat=4.170e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.863e-04 U_stat=4.170e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.950e-04 U_stat=4.360e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.759e-07 U_stat=4.470e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.821e-01 U_stat=2.320e+02
https://www.proteinatlas.org/ENSG00000108179-PPIF/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.792e-03 U_stat=3.430e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.236e-03 U_stat=3.990e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.237e-03 U_stat=3.950e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.604e-03 U_stat=3.640e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.469e-01 U_stat=2.020e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000002726-AOC1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.691e-05 U_stat=3.800e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.075e-03 U_stat=3.850e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.385e-03 U_stat=4.110e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.180e-05 U_stat=4.110e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.544e-01 U_stat=2.970e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000148344-PTGES/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.620e-05 U_stat=3.820e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.463e-03 U_stat=3.980e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.072e-04 U_stat=4.270e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.868e-06 U_stat=4.250e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000149418-ST14/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.720e-04 U_stat=3.690e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.314e-02 U_stat=3.770e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.463e-03 U_stat=3.980e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.679e-05 U_stat=4.090e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.637e-01 U_stat=2.960e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000127838-PNKD/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                     TMDE	                                      
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                                     Top 5	                                     
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.716e-05 U_stat=4.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.745e-05 U_stat=5.500e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.685e-05 U_stat=6.300e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.558e-04 U_stat=6.400e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000101871-MID1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.742e-05 U_stat=4.500e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.164e-04 U_stat=9.400e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.931e-05 U_stat=7.000e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.392e-02 U_stat=1.210e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.599e-01 U_stat=1.810e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000119640-ACYP1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.610e-04 U_stat=7.600e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.754e-02 U_stat=1.800e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.314e-02 U_stat=1.410e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.014e-04 U_stat=7.700e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.342e-01 U_stat=2.230e+02
https://www.proteinatlas.org/ENSG00000154217-PITPNC1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.486e-03 U_stat=9.000e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.383e-02 U_stat=1.630e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.110e-03 U_stat=1.040e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.232e-04 U_stat=7.200e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.478e-03 U_stat=3.710e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000151364-KCTD14/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.281e-03 U_stat=8.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.721e-03 U_stat=1.360e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.799e-05 U_stat=6.800e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.649e-03 U_stat=1.050e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.138e-01 U_stat=2.150e+02
https://www.proteinatlas.org/ENSG00000182621-PLCB1/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                   Bottom 5	                                    
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.318e-04 U_stat=3.570e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.196e-03 U_stat=4.130e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.863e-04 U_stat=4.170e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.354e-04 U_stat=3.720e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.857e-01 U_stat=2.130e+02
https://www.proteinatlas.org/ENSG00000160678-S100A1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.497e-06 U_stat=4.080e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.572e-02 U_stat=3.590e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.611e-02 U_stat=3.500e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.215e-06 U_stat=4.320e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.508e-01 U_stat=2.360e+02
https://www.proteinatlas.org/ENSG00000114923-SLC4A3/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.215e-06 U_stat=4.090e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.423e-05 U_stat=4.530e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.441e-05 U_stat=4.650e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.113e-06 U_stat=4.290e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.877e-01 U_stat=2.700e+02
https://www.proteinatlas.org/ENSG00000108639-SYNGR2/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.281e-03 U_stat=3.470e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.142e-03 U_stat=3.830e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.588e-01 U_stat=3.130e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.323e-03 U_stat=3.510e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.450e+02
https://www.proteinatlas.org/ENSG00000213512-GBP7/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.176e-03 U_stat=3.480e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.463e-03 U_stat=3.980e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.527e-03 U_stat=3.940e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.120e-03 U_stat=3.440e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.585e-01 U_stat=2.110e+02
https://www.proteinatlas.org/ENSG00000102699-PARP4/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                      MDS	                                      
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                                     Top 5	                                     
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.896e-04 U_stat=6.100e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.566e-02 U_stat=1.440e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.463e-03 U_stat=1.200e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.
No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.558e-04 U_stat=6.400e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.074e-02 U_stat=3.500e+02
https://www.proteinatlas.org/ENSG00000074527-NTN4/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.281e-03 U_stat=8.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.208e-01 U_stat=1.850e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.217e-02 U_stat=1.570e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.481e-03 U_stat=9.000e+01
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.138e-01 U_stat=2.750e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

https://www.proteinatlas.org/ENSG00000139344-AMDHD1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.289e-03 U_stat=1.020e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.475e-01 U_stat=2.300e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.345e-02 U_stat=1.670e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.655e-01 U_stat=1.790e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.186e-03 U_stat=3.920e+02
https://www.proteinatlas.org/ENSG00000173598-NUDT4/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.088e-04 U_stat=6.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.411e-01 U_stat=2.690e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.331e-01 U_stat=2.020e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.736e-03 U_stat=9.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.576e-01 U_stat=2.180e+02
https://www.proteinatlas.org/ENSG00000005108-THSD7A/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.839e-03 U_stat=1.010e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.800e-02 U_stat=1.750e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.133e-03 U_stat=1.130e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.222e-02 U_stat=1.190e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.357e-01 U_stat=2.890e+02
https://www.proteinatlas.org/ENSG00000127955-GNAI1/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                   Bottom 5	                                    
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.129e-05 U_stat=3.810e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.799e-05 U_stat=4.500e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.361e-05 U_stat=4.560e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.679e-05 U_stat=4.090e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.787e-04 U_stat=8.900e+01
https://www.proteinatlas.org/ENSG00000130413-STK33/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.560e-04 U_stat=3.700e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.659e-02 U_stat=3.730e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.198e-04 U_stat=4.300e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.876e-04 U_stat=3.890e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.295e-01 U_stat=3.140e+02
https://www.proteinatlas.org/ENSG00000145626-UGT3A1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.293e-03 U_stat=3.400e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.539e-02 U_stat=3.410e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.757e-02 U_stat=3.720e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.031e-03 U_stat=3.610e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.637e-01 U_stat=1.940e+02
https://www.proteinatlas.org/ENSG00000159166-LAD1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.024e-03 U_stat=3.300e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.289e-03 U_stat=4.040e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.039e-04 U_stat=4.220e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.736e-03 U_stat=3.630e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.788e-02 U_stat=3.280e+02
https://www.proteinatlas.org/ENSG00000099812-MISP/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.079e-03 U_stat=3.490e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.121e-03 U_stat=3.870e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.602e-03 U_stat=4.090e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.071e-03 U_stat=3.690e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

BAP1 v.s. PBRM1: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.856e-01 U_stat=2.380e+02
https://www.proteinatlas.org/ENSG00000182795-C1orf116/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                      MDE	                                      
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                                     Top 5	                                     
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.174e-04 U_stat=4.020e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.202e-03 U_stat=1.280e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.734e-03 U_stat=1.180e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.254e-03 U_stat=1.040e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.684e-02 U_stat=1.650e+02
https://www.proteinatlas.org/ENSG00000136231-IGF2BP3/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.170e-03 U_stat=3.660e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.905e-02 U_stat=1.810e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.418e-01 U_stat=2.080e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.287e-03 U_stat=1.140e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.102e-02 U_stat=3.500e+02
https://www.proteinatlas.org/ENSG00000242515-UGT1A10/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.883e-04 U_stat=3.830e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.038e-02 U_stat=1.620e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.057e-03 U_stat=1.320e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.564e-03 U_stat=1.150e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.849e-01 U_stat=2.390e+02
https://www.proteinatlas.org/ENSG00000100097-LGALS1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.615e-03 U_stat=3.700e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.711e-04 U_stat=1.090e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.057e-03 U_stat=1.320e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.510e-02 U_stat=1.650e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.567e-02 U_stat=1.330e+02
https://www.proteinatlas.org/ENSG00000170231-FABP6/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.740e-03 U_stat=3.690e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.990e-01 U_stat=2.180e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.813e-02 U_stat=1.980e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.627e-04 U_stat=7.400e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.479e-03 U_stat=1.080e+02
https://www.proteinatlas.org/ENSG00000122884-P4HA1/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                   Bottom 5	                                    
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.023e-03 U_stat=7.400e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.016e-04 U_stat=4.800e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.846e-03 U_stat=4.570e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.330e-03 U_stat=4.070e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.934e-01 U_stat=2.330e+02
https://www.proteinatlas.org/ENSG00000179403-VWA1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.987e-04 U_stat=5.400e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.111e-04 U_stat=4.890e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.670e-02 U_stat=4.180e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.553e-02 U_stat=3.810e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.203e-01 U_stat=2.780e+02
https://www.proteinatlas.org/ENSG00000179144-GIMAP7/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.498e-03 U_stat=7.900e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.673e-03 U_stat=4.510e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.819e-02 U_stat=3.910e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.197e-03 U_stat=3.970e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.791e-01 U_stat=2.970e+02
https://www.proteinatlas.org/ENSG00000164116-GUCY1A1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.873e-03 U_stat=8.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.434e-02 U_stat=4.210e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.588e-02 U_stat=4.190e+02
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04


No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.834e-03 U_stat=3.980e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.921e-01 U_stat=2.260e+02
https://www.proteinatlas.org/ENSG00000061337-LZTS1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.498e-03 U_stat=7.900e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.181e-03 U_stat=4.640e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.959e-04 U_stat=4.700e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.974e-03 U_stat=4.150e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.426e-01 U_stat=3.260e+02
https://www.proteinatlas.org/ENSG00000173269-MMRN2/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                     TPDE	                                      
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
                                     Top 5	                                     
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.911e-04 U_stat=6.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.711e-04 U_stat=1.090e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.181e-03 U_stat=1.120e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.197e-03 U_stat=1.200e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.014e-01 U_stat=2.110e+02
https://www.proteinatlas.org/ENSG00000071539-TRIP13/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.873e-03 U_stat=8.200e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.412e-01 U_stat=2.360e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.484e-01 U_stat=2.840e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.177e-02 U_stat=1.310e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=8.005e-01 U_stat=2.400e+02
https://www.proteinatlas.org/ENSG00000133488-SEC14L4/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.740e-03 U_stat=8.100e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.215e-01 U_stat=2.440e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.019e-01 U_stat=1.990e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.391e-02 U_stat=1.340e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.124e-01 U_stat=1.740e+02
https://www.proteinatlas.org/ENSG00000175063-UBE2C/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=6.169e-03 U_stat=9.900e+01

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.761e-02 U_stat=1.750e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.168e-03 U_stat=1.420e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.306e-02 U_stat=1.560e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.530e+02
https://www.proteinatlas.org/ENSG00000128335-APOL2/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.039e-03 U_stat=1.010e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.358e-02 U_stat=1.650e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=5.414e-03 U_stat=1.370e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.034e-01 U_stat=1.760e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.530e+02
https://www.proteinatlas.org/ENSG00000265190-ANXA8/pathology/renal+cancer/KIRC

--------------------------------------------------------------------------------
                                   Bottom 5	                                    
--------------------------------------------------------------------------------
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=9.812e-05 U_stat=4.040e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.027e-04 U_stat=4.840e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=4.557e-03 U_stat=4.420e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.099e-04 U_stat=4.540e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.530e+02
https://www.proteinatlas.org/ENSG00000261371-PECAM1/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.174e-04 U_stat=4.020e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=3.251e-04 U_stat=4.830e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.846e-03 U_stat=4.570e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=2.627e-04 U_stat=4.430e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.378e-03 U_stat=1.200e+02
https://www.proteinatlas.org/ENSG00000064989-CALCRL/pathology/renal+cancer/KIRC

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.174e-04 U_stat=4.020e+02

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.181e-03 U_stat=4.640e+02
Protein
p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=7.467e-04 U_stat=4.290e+02
RNA

No artists with labels found to put in legend.  Note that artists whose label start with an underscore are ignored when legend() is called with no argument.

p-value annotation legend:
ns: 5.00e-02 < p <= 1.00e+00
*: 1.00e-02 < p <= 5.00e-02
**: 1.00e-03 < p <= 1.00e-02
***: 1.00e-04 < p <= 1.00e-03
****: p <= 1.00e-04

Stage I v.s. Stage IV: Mann-Whitney-Wilcoxon test two-sided with Bonferroni correction, P_val=1.000e+00 U_stat=2.530e+02
https://www.proteinatlas.org/ENSG00000176435-CLEC14A/pathology/renal+cancer/KIRC

KeyboardInterrupt

Perform GSEA using fGSEA¶

We need to save in the correct format and the re-read all in and save as a summary file (since it otherwise takes too long to look at every file).


conds = c('Stage1-Stage4',  'young-old', 'PBRM1-Female', 'middle-old',  'Random0.1-Random1.1', 'Random0.2-Random1.2', 'Random0.3-Random1.3', 'Random0.4-Random1.4')

for (cases_conds in conds) {
  for (r in reg_grps) {
    sircleFileName <- paste0('../data/S050_CCRCC_Clark_Cell2019/sircle/all_patients/all_cpgs/Integration/output_data/GSEA/', r, '-IntegrationModel-stats-',cases_conds ,'-.csv')
    # https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-587
    vis_df <- read.csv(sircleFileName)

    # Run GSEA on the consistently changed genes between late and early stage using the t-stat as the rank
    GSEA_results <- GSEASetupSircle(vis_df, paste0(cases_conds, " ", r), gene_name="hgnc_symbol", stat='diff',   GSEA_file_dir=GSEA_file_dir, output_dir='../data/S050_CCRCC_Clark_Cell2019/sircle/all_patients/all_cpgs/Integration/output_data/GSEA/', pathway_list=pathway_list)
  }

}

https://www.nature.com/articles/s41581-020-00359-2/figures/6

In [22]:
gsea_dir = f'{output_dir}Integrated_fGSEA/fGSEA/' #output_dir = f'{base_dir}sircle/F6_integrative_comparisons/'

---------------------------------------------------------------------------
NameError                                 Traceback (most recent call last)
Input In [22], in <cell line: 1>()
----> 1 gsea_dir

NameError: name 'gsea_dir' is not defined

Consolidate GSEA into single file for supps¶

In [24]:
import os
from sciutil import SciUtil
u = SciUtil()
rcm_labels = ["MDS", "MDS_TMDE", "MDE", "MDE_TMDS", "TMDE", "TMDS", "TPDE", "TPDE_TMDS",  "TPDS", "TPDS_TMDE"]

files = os.listdir(f'{output_dir}Integrated_fGSEA/fGSEA/')
# Read through each one and print out each of the various
# Read through each one and print out each of the various
comparisons = ['PBRM1-BAP1', 'Stage IV-Stage I', 'old-young']
comp_map = {'mutation': 'PBRM1-BAP1', 'S4-S1': 'Stage IV-Stage I', 'age': 'old-young'}
for comp in comparisons:
    with open( f'{output_dir}Integrated_fGSEA/{comp}_consolidated_metabolic_GSEA.tsv', 'w+') as fout:
        fout.write(f'Comparison\tRegulation_Grouping_2\tPathway\t fGSEA NES\t fGSEA padj\t fGSEA pval \t fGSEA size\n')
        for f in files:
            if comp == 'Stage IV-Stage I':
                f_name = f.replace('Stage_IV-Stage_I', 'Stage IV-Stage I')
            else:
                f_name = f
            f_name = '_'.join(f_name.split('_')[1:])
            if 'MetabolicPathways.csv' in f_name and comp == f_name.split('_')[0]:
                f_s = f_name.split('_')
                if f_s[1] in rcm_labels:
                    if f_s[2] == 'GSEA':
                        reg_label = f_s[1]
                    else:
                        reg_label = f_s[1] + '&' + f_s[2]
                    gsea = pd.read_csv(f'{output_dir}Integrated_fGSEA/fGSEA/{f}')
                    sig_gsea = gsea
                    # Make sure the size is > 3
                    sig_gsea = sig_gsea.sort_values(by='NES')
                    for i, g in enumerate(sig_gsea['pathway'].values):
                        fout.write(f'{comp}\t{reg_label}\t{g}\t{sig_gsea["NES"].values[i]}\t{sig_gsea["padj"].values[i]}\t{sig_gsea["pval"].values[i]}\t{sig_gsea["size"].values[i]}\n')